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Cytoscape User Manual

1. BINDhuman sif Network of all human protein protein interactions in the BIND database as of Dec 2006 yeastHighQuality sif Sample molecular interaction network file interactome_merged networkTable gz Human interactome network file in tab de limited format sampleStyles props Additional sample Visual Styles From Ideker et al Science 292 929 2001 Obtained from data hosted at http www blueprint org bind bind_downloads html From von Mering et al Nature 417 399 2002 and Lee et al Science 298 799 2002 ok Created from Cytoscape tutorial web page Original data sets are available at http www cyto scape org cgi bin moin cgi Data_Sets from A merged human interactome by Andrew Garrow Yeyejide Adeleye and Guy Warner Unilever Safety and Environmental Assurance Center Launch the application Double click on the icon created by the installer or by running cytoscape sh from the command line Linux or Mac OS X or double clicking cytoscape bat Windows Alternatively you can pass the jar file to Java directly using the command java Xmx512M jar cytoscape jar p plugins Cytoscape User Manual The Xmx512M flag tells java to allocate more memory for Cytoscape and the p plugins option tells cytoscape to load all of the plugins in the plugins directory Loading the plugins is important because many key features like layouts filters and the attribute browser are included with Cytoscape a
2. The Boolean Meta Filter allows you to define a new filter that is a logical combination of existing filters Available filters are displayed By selecting one or more filters you can then choose whether Nodes or Edges pass ALL AND AT LEAST ONE OR or ONLY ONE XOR of the selected filters Once created Boolean filters can then themselves be combined using the Boolean filter to create arbitrarily complex logical combinations of filters Note that unlike the String and Numerical Filters Boolean filters will need to be assigned a name manually Saving Filters Filters are currently saved automatically inthe filters props file found in the cytoscape directory found in each user s home directory Once created filters are saved for future sessions as long as you exit Cytoscape normally via File Quit 1 e not via ctrl c on Linux Running filters Any available filter can be run by pressing the Apply selected filter button When a filter is applied to your network and multiple nodes or edges are selected all of the normal selection related operations may be performed such as Delete Selected Node Edges Copy To New Network and Invert Selection The Select Menu The Select Nodes and Select Edges menus provide several mechanisms for selecting nodes and edges Most options are fairly straightforward however some need extra explanation Select gt Nodes gt By Name selects nodes by the node iden
3. Gene Association file for Saccharomyces cerevisiae ad Gene Association file for Drosophila melanogaster vanced ig Gene Association file for Mus musculus Show Mapping g Gene Association file for Arabidopsis thaliana Lal Gene Association file for Caenorhabditis elegans Gel Gene Association file for Rattus norvegicus d Gene Assqdu Gene Association file for Oryza sativa Ontology IER Select File Import Ontology and Annotation to open the Import Ontology and Annotation window From the Annotation dropdown list select a gene association file for your network For example if you want to annotate the yeast network select Gene Association file for Saccharomyces cerevisiae 161 Cytoscape User Manual Step 2 Select an Ontology File Ontology Gene Ontology Full vanced Ga Generic GO slim Show Mapping Yeast GO slim Molecule role NOH Protein name family name ontology Even QU Event NOH pathway ontology ft Click Edit Protein protein interaction Select an Ontology data OBO file from the Ontology dropdown list If the file 1s not loaded yet it will be shown in red The first three files are Gene Ontology files You can load other ontologies but you need your own annotation file to annotate networks Step 3 Import the files Once you click the Import button Cytoscape will start loading OBO and Gene Association files from the remote sources If you choose GO Full it may tak
4. 76 Cytoscape User Manual EJ Layout Settings Layout Algorithm Force Directed Layout Force Directed Layout Settings Default Spring Coefficient Default Spring Length Default Node Mass Number of Iterations The minimum edge weight to consider The maximum edge weight to consider 8623157E308 Integration algorithm to use gt Only layout selected nodes a AJ E 3 ua iD Ee E sc c I A Fa El le e EJ LA ejlelejo The edge attribute that contains the weights unweightec e Manual Layout The simplest method to manually organize a network is to click on a node and drag it If you select multiple nodes all of the selected nodes will be moved together Rotate CytoPanel 5 Ki Warum Scale H b Rotate in Degrees 90 180 270 360 Rotate Selected Node Selecting the Layout Rotate option will open the Rotate window in CytoPanel 5 This function will either rotate the entire network or a selected portion of the network The image below shows a network with selected nodes rotated Before 71 Cytoscape User Manual sample e CytoPanel 5 Rotate in Degrees 0 90 180 270 360 Y Rotate Selected Node E After AAA sample e CytoPanel 5 Rotate in Degrees 0 90 180 270 360 Y Rotate Selected Node E Scale CytoPanel 5 Tul Rotate b Scale HS 1 81 41 2 1 2 4 8 Scale Selected Nodes Only Selecting th
5. force directed paradigm as implemented by Kamada and Kawai 1988 Network nodes are treated like physical objects that repel each other such as electrons The connections between nodes are treated like metal springs attached to the pair of nodes These springs repel or attract their end points according to a force function The layout algorithm sets the positions of the nodes in a way that minimizes the sum of forces in the network This algorithm can be applied to the entire network or a portion of it by selecting the appropriate options from Layout Cytoscape Layouts Spring Embedded A sample screen shot is provided below 71 Cytoscape User Manual Attribute Circle Layout The attribute circle layout is a quick useful layout particularly for small networks that will locate all of the nodes in the network around a circle The node order is determined by a user selected node attribute The result is that all nodes with the same value for that attribute are located together around the circle Using Layout gt Cytoscape Layouts Attribute Circle Layout attribute to put all nodes around a circle using attribute to position them The sample screen shot below shows the a subset of the galFiltered network organized by node Degree T2 Cytoscape User Manual Group Attributes Layout The group attributes layout is similar to the attribute circle layout described above except that instead of a single circle with all of th
6. the menus Hover the mouse pointer over an icon and wait momentarily for a description to appear as a tooltip The network management panel top left panel This contains an optional network overview pane shown at the bottom left The main network view window which displays the network The attribute browser panel bottom panel which displays attributes of selected nodes and edges and enables you to modify the values of attributes 13 Cytoscape User Manual The network management and attribute browser panels are dockable tabbed panels known as CytoPanels You can undock any of these panels by clicking on the Float Window control in the upper right corner of the CytoPanel If you select this control e g on the attribute browser panel you will now have two Cytoscape windows the main window and a new window labeled CytoPanel 2 similar to the one shown below Popup will be displayed when you put the mouse pointer on a cell Data Panel B d b Hee IL alias annotation DA Object Marne annotranon Taxon YILO ZA 3 phosphoglyoe F 3 pho sphog Woe rate d ehyd rogenase Saccha romyces cerevisiae YCRO12W 3 phosphoglycer 3 phosphoghcerate kinase Saccharomyces cerevisiae YOL136 PFK 2 6 phosph 6 phosphotructa 2 kinase PFK 2 Saccharomyces cerevisiae YPROTOC RNA polymerase A135 RNA polymerase subunit Saccharomyces cerevisiae YPRIISM B type cyclin CL B type cyclin iccharomyces cerevisiae YER135W CKS1 Cdc28 pro Cdc 3
7. Cytoscape User Manual Table of Contents C VIOSCapE User Mandak ee pe a ee ee ee 3 TET ORIN DOM ee euere ee 48 DEV TODE E 4 Bec asec 4 bdo S E e ER 4 Please Cite lbs sci IE Jt RTE 1 16 210 PA er ee ee ee 8 System regure MENS EE 8 Se o AA nn A EEE 56 ore Milit er P m TTE 12 ju Xu 15 Network MAMAS eie D sus eric eds 18 The Network Overview Window oooocccccncoconcncocononconononno nono noo e heme esses ses essen EEE ES 20 Command Ire AT UNEIS Ae 21 Cy OSC ae is ast II Dr in oe ee 22 Manas ne Properties eege 22 Managing Bookmarks an ea eege 24 Manani PEOX SS Nennen nee een 24 e 24 Import F xed Format Network Piles usarse eu 25 Import Free Format Table Piles ua ann ac ine 26 Import Networks irom Web SEIVIES nn eege 30 Et ac New ING LW este a ea ne a nds cathe toda ados NAE 30 Supported Network File Formats uses een 3l SIR e Losses is iesus ee ad een UE MM engere 31 INNE c 33 E Ion c omecns 38 XGOMML POEMA ET 38 SBML Systems Biology Markup Language Format 39 BioPAX Biological PAthways eXchange Format 39 AP uu uA 39 Delimited Text Table and Excel Workbook 39 Node Naming I
8. Ic Erfrscere in Falbwirz Gear T age Tops Age YHLOOEE Froe ECC paliw MARK aan Greg Clacede iniuced Fas anal RES an lid sinas Edge Tarper arrow vu HEI ES LO 134 i Clacese indured Ras aciem Def Label Spring Cueffichera DS Edge Target Aren TLLO2EW jES0E1 1 a The Irasipar sir er TPO 3 Defan Labal Spring Lareyh a Detap Hroie Haag Zo E Teale Number at heran 300 Piode Barcer Color d pra on aren bo uER Runge Kutta e Hack Band acte 1 1 AR Pret Me rape penam of all nodes Madi caor Mode Attriberie Browser Boge Anria Browser k iert Antia Area T Waremme io Syicacape z 5d Rig i rlrk drag sa 00M Mickils r ck drag ta FAM A Lai a E i k L Sea JGraph Layouts Several other alignment algorithms including a selection from the JGraph project http jgraph source forge net are also available under the Layout menu Layout Parameters Many layouts have adjustable parameters that are exposed through the Layouts Settings menu option This will pop up the following dialog which allows you to choose which layout algorithm settings to adjust The settings presented vary by algorithm and only those algorithms that allow access to their parameters will appear in the drop down menu at the top of the dialog Once you ve modified a parameter clicking the Execute Layout button will apply the layout This be repeated until a useful layout is achieved Settings can be saved using the Save Settings button
9. elif goOntology F molfunc write np np s np np s n np np printName goID Appendix B GNU Lesser General Public License GNU LESSER GENERAL PUBLIC LICENSE Version 2 1 February 1999 Copyright C 1991 1999 Free Software Foundation Inc 59 Temple Place Suite 330 Boston MA 02111 1307 USA Everyone is permitted to copy and distribute verbatim copies of this license document but changing it is not allowed This is the first released version of the Lesser GPL It also counts as the successor of the GNU Library Public License version 2 hence the version number 2 1 Preamble The licenses for most software are designed to take away your freedom to share and change it By contrast the GNU General Public Licenses are intended to guarantee your freedom to share and change free software to make sure the software 1s free for all its users This license the Lesser General Public License applies to some specially designated software packages typically libraries of the Free Software Foundation and other authors who decide to use it You can use it too but we suggest you first think carefully about whether this license or the ordinary General Public License is the better strategy to use in any particular case based on the explanations below When we speak of free software we are referring to freedom of use not price Our General Public Licenses are designed to make sure that you have the freedom to distribute c
10. gree ce AA ki LHET Ei A T da Pp AAA ROA AO L t Mr IE A a E A raue ADS ee ehr er risa de Prid rad a Se ed a jor det Tits Doreen of tae dae peed fe DA az Dp ea a A AT de i rece coat inis Mi el TERT Tbr p Pe Dea LAB LL MEUS Lo el Wii anms rn aj eR ans Mp Las Color This Mules Seer ee Sai ke EAA regu Thre AE tee et So LEM TRIGA hare A Kan Ah rg o A gei rp p h camera eS nis Hf ds dde rs rra geri ba k t Too TLE LOW Petts tute ron m fn o TER porte boda poor Keen ECH mern ren k n Lagu Paya F TELA ee He o Eih pa abs Mash Gne H y a Wed Pina faisa t Nod kiirii Fostar l p here bosi Mateces Aria osar 151 Cytoscape User Manual Basic Usage Cytoscape includes four CytoPanels Control Panel on the left Tool Panel on the bottom of Control Panel Data Panel on the bottom and Result Panel on the right By default Control Panel and Data Panel will appear Result Panel may appear depending on the mix of Cytoscape plugins that you currently have installed Tool Panel will appear when you select the following commands under the Layout menu Rotate Scale and Align and Distribute All panels can be shown or hidden using the View Show Hide functions Wm Select Layout P Hide Control Panel Hide Data Panel Show Results Panel Open VIZ Map pe pra In addition CytoPanels can be floated or docked by selecting the icon at the top right corner of each CytoPanel The icon and tooltip will chang
11. 2009906 508093 e e e ee eee amp y ek le Tess is in xt Ke imp sh e e e bh a oo yFiles Hierarchical Layout The hierarchical layout algorithm is good for representing main direction or flow within a network Nodes are placed in hierarchically arranged layers and the ordering of the nodes within each layer is chosen in such a way that minimizes the number of edge crossings This algorithm 1s available by selecting Layout gt yFiles gt Hierarchical 68 Cytoscape User Manual 0 000 sample ki a E Fa ae a 2 l CS X Qu ef Gs ef p E es t I d LONE ze S e e po a LI N e yFiles Organic Layout The organic layout algorithm is a kind of spring embedded algorithm that combines elements of the other algorithms to show the clustered structure of a graph This algorithm is available by selecting Layout gt yFiles gt Organic Select Layout Plugins Help WS pol o C Scale Align and Distribute 1 yFiles d Circular Minimize Edge Crossings for Selected Nodes YU Organic Cytoscape Layouts k Hierarchic JGraph Layouts k Random MirrorX MirrorY el u Cytoscape Layouts Cytoscape Layouts are those layouts that have been written or integrated by Cytoscape developers These layouts are fully integrated with Cytoscape All Cytoscape Layouts have the option to operate on only the selected nodes and all provide a Settings panel to change the parameters of the algorit
12. A sample screenshot is below 118 Cytoscape User Manual e rra riim m S AS Sari diria Eple y ppe Tep i ip l on mi H imr mu a a bag CH G h g aH a a l li Car I LIL Li Tn A 1m A Tutorial 4 How to Use Utilities for Discrete Mappers The following tutorial demonstrates new features in Cytoscape 2 5 The new VizMapper user interface has some utilities to help users editing discrete mappings The goal of this section is learning how to set and adjust values for discrete mappings automatically 1 Load a sample network From the main menu select File Import gt Network and select sampleData galFiltered sif 2 Apply layout to the network From the main menu select Layout Cytoscape Layouts Degree Sorted Circle Layout This layout algorithm sort nodes in a circle by degree of the nodes Degrees will be stored as node attribute names Degree after you applied this algorithm 3C 1 i c k t h e Vi z M a p a e button on the tool bar 4 Click Defaults panel on the VizMapper main panel Default Apearence Editor pops up see below 5 Edit the following visual properties and press Apply Since you changed opacity of the node you can see the nodes bihind the front node see below Node Oppacity 100 Edge Color White Background Color Black 119 Cytoscape User Manual m8 Cytoscape Desktop New Session SE LJ Q e EX amp E a MI Corirol Para LT ana galFiltered sif Ll Network Viz
13. HOB ice Oi icial Symbol Gereh Pathway Fhenotypes 7991 TUSCS 9433 STK11 19p13 and TP53 might playar I Prostate cancer susceptibory ta 5 70 PIER Observational study and meta analysis of gene EEGG pathway Adherens junction KEGG path Abdominal body fat distribution m 4595 MUTYH Observational study of gene disease assodato Reactome Event DNA Repair Ade nomas multiple colorectal Color 100 ADA Observational study of gene disease associato KEGG pathway Purine metabolism Reactome Adenosine deaminase deficiency par 7157 TPS3 PS3 mediated regulation of metallothionein tra RECO pathway Amyotrophic lateral sclerosis Adrenal cortical carcinoma Breast cai 5830 FEXS the N Terminus of Fex5p is required for redirec Ad remite ud ystrophry neonatal Zell 2670 GFAP An adui form of Alexander disease a novel m KEGG pathway Neuradegenerative Disorders Alexander disease 642 ELM M eta analysis of gene disease associapon Hu Alzheimer disease usceptibisty va 5663 FSEN1 Observational study of gene disease associatio KEGG pathway Alzheimer s disease KEGG par Alzheimer disease type 3 Alzheimer 5664 FSEN Observational study of gene disease associatio KEGG pathway Alzheimer s disease KEGG pat Alzheimer disease 4 Cardiomyopath 1639 DCTNI Observational study of gene disease associatio KEGG pathway pathway e lateral sclerosis suscegt 7337 UBE 3A Observational study
14. attributes To browse those attributes please use the attribute browser see the example below D w D proa oa nans crol op def GOOF 28 nuclear chrpenzseme A chramasome Touncd in tee nurieus of a eukaryotic cell G OEDOREE Z9 Shane chramosore A chremoasame Tung in rea Oo GCHD00535375 celular comporti The par of a cell or itz extracellular err onmgnt in which a gene prodoo iz lcabad A gane prodoo may ba located in ona or LGCEDIMESS 76 exiracelular region The space externa bs the gujemmast siructure ar a ce For cells without externa precie pr external encapsulating siructune G OkEDOQS3578 sxiracelilar marik anu he Ha A laar cansisting Mairi ef nrersins iaspecialy cola and gkent mmome ats ment as Gece rar forms a 550061 00005615 exiracdlular space Thai part of a miiicellular organem cuide ca cells proper usuallyiaken to be putzice the plasma membranes and GC 100005418 fell wall The rigid er semi rigid emalii hing guiside ihe dell mere of plam Tungal and mos prakargoix cel raintsinmg Iher Gr sse imrzcelladar The ihig content af a call hie marter camalrad wihie du noc uding the plasrea mambrans wasal raian la ake k ds lar GOOD cell The basic siructural and Tuncilonal en of all organisms includes ihe plasma membrane and army externa encapsulating siruci GCEDOU A34 nune a meenbrane Dounced organes ar eukawtrt Cells in ch chrome arme nauseam and replkcaec ie rl celis pne nuce CGrkOQS635 nuclear armada pal The dobia lipid bizar enciasing th
15. java lang Integer or Integer for integer values etc If the value is actually a list of values the class should be the type of the objects in the list If no class is specified in the header line Cytoscape will attempt to guess the type from the first value If the first value contains numbers in a floating point format Cytoscape will assume java lang Double if the first value contains only numbers with no decimal point Cytoscape will assume java lang Integer otherwise Cytoscape will assume java lang String Note that the first value can lead Cytoscape astray for example floatingPointAttribute firstName 1 secondName 2 5 In this case the first value will make Cytoscape think the values should be integers when in fact they should be floating point numbers It s safest to explicitly specify the value type to prevent confusion A better format would be 42 Cytoscape User Manual floatingPointAttribute class Double firstName 1 secondName 2 5 Or floatingPointAttribute firstName 1 0 secondName 2 5 Every line past the first line identifies the name of an object a node in a node attribute file or an edge in a edge attribute file along with the String representation of the attribute value The delimiter is always an equals sign whitespace spaces and or tabs before and after the equals sign is ignored This means that your names and values can contain whitespace but object names cannot contain an equals sign and no
16. nodes with their common gene names 2 Discrete Mapper Discrete network attributes are mapped to discrete visual attributes For example a discrete mapper can map all protein protein interactions to the color blue 3 Continuous Mapper Continuous graph attributes are mapped to visual attributes Depending on the visual attribute there are three kinds of continuous mappers i Continuous to Continuous Mapper for example you can map a continuous numerical value to a node size 101 Cytoscape User Manual ii Color Gradient Mapper This is a special case of continuous to continuous mapping Continuous numerical values are mapped to a color gradient iii Continuous to Discrete Mapper for example all values below 0 are mapped to square nodes and all values above 0 are mapped to circular nodes However note that there is no way to smoothly morph between circular nodes and square nodes The table below shows visual mapper support for each visual property Legend Symbol NEU Mapping is not supported for the specified visual property Mapping is fully supported for the specified visual property Mapping is partially supported for the specified visual property Support for continuous to continuous mapping is not supported Node Visual Mappings per e Border Co e Border Op e Label Opa e Line Width e Font Fami Node Opacity e e l Numeric Node Size Width Height Node Font Size Wi F Node Visual Pr
17. 0004362 glutathione reductase NADPH isa 0015038 0015933 0016209 0016654 0017019 myosin phosphatase catalyst partof 0017018 A second example KEGG pathway ontology curator KEGG type Metabolic Pathways 90001 Metabolism 80001 Carbohydrate Metabolism isa 90001 80003 Lipid Metabolism isa 90001 80002 Energy Metabolism isa 90001 80004 Nucleotide Metabolism isa 90001 80005 Amino Acid Metabolism isa 90001 80006 Metabolism of Other Amino Acids isa 90001 80007 Metabolism of Complex Carbohydrates isa 90001 168 Cytoscape User Manual The format has these required features The first line contains two parenthesized assignments for curator and type In the GO example above the ontology file which is created from the XML that GO provides nests all three specific onto logies molecular function biological process cellular component below the root ontology named Gene Ontology type all tells you that all three ontologies are included in that file Following the mandatory title line there are one or more category lines each with the form numberO name isa partof numberl number2 where isa and partof are terms used in GO they describe the relation between parent and child terms in the ontology hierarchy The trailing blank before each left square bracket is not required it is an artifact of the python script that creates these files The Annotation F
18. EIGG pathagy PPAR orale Guay HET E ben WUM 1 HDCT UA bag WWE domam cerei f LisFrageranl yd rome B par Pues ipei 1 com i OCG LT porc ore Gr ng ee Fumo REDD pura a prior a ras h Multiple malignancy pymdrormmre poer Fe imageg el PLA pala ARM Pato EIDO pathagy Noh ora lr patbegy Apart a ros meinen DOT h D page careinoca s enm CX 1L a bra Se L2 Dor Cprain L PASA IL ee ee ad nm DOHA Zo fete tbo E ELE E Prania BE para AH ene vrbi war Diosa Di ran bk ao has ra Poche D Friden ral erging ech D ccr DARA gegen ef ECTS ROR andi ET e i Pare Peat Carty prn TTT E l EE EXA Thyrald carcinoma a 5 annt Node Antribute ra dee AStribote Dome Network AStribote roanier e po Cette 2 60 Rach perl x day To Zap Mide e dr te PAX Navigation and Layout Basic Network Navigation Cytoscape uses a Zoomable User Interface for navigating and viewing networks ZUls use two mechanisms for navigation zooming and panning Zooming increases or decreases the magnification of a view based on how much or how little a user wants to see Panning allows users to move the focus of a screen to dif ferent parts of a view Zoom Cytoscape provides two mechanisms for zooming either using mouse gestures or buttons on the toolbar Use the zooming buttons located on the toolbar to zoom in and out of the interaction network shown in the current network display Zoom icons
19. Graphics is just a new type of Visual Properties and you can use them from standard VizMap user interface There are nine Custom Graphics Visual Properties Node Custom Graphics 1 9 and they will be displayed in the standard VizMap Default View Editor or Mapping Editors Custom Graphics Positions Each Custom Graphics Visual Property is associated with a position You can edit position of them using same Ul as Label Position 108 Cytoscape User Manual Z Ordering Number after Custom Graphics Visual Property represents order of layers Basic node color and shape are always rendered first then Node Custom Graphics I 2 and 9 Force to Resize Custom Graphics to Node Size Default Appearance for default vi Lock Node Width Height Make Arrow Color Match Edge Color vi Synchronize Custom Graphics Size to Node Size Create Node Label Color from Node Color Mode Edge Global Dependencies By default Custom Graphics objects are automatically resized to Node Size Visual Property To control Custom Graphics size separately you need to uncheck Synchronize Custom Graphics Size to Node Size dependency You can find this check box in Default Editor s Dependencies panel 109 Cytoscape User Manual Custom Graphics Selector Select Hew Value Remove Graphics database global network injection Cancel To select an Custom Graphics just click one of them and press Apply T
20. Hood lab the University of California San Diego Trey Ideker lab Memorial Sloan Kettering Cancer Center Chris Sander lab the Institut Pasteur Benno Schwikowski lab Agilent Technologies Annette Adler lab and the University of California San Francisco Bruce Conklin lab Visit http www cytoscape org for more information License Cytoscape is protected under the GNU LGPL Lesser General Public License The License is included as an appendix to this manual but can also be found online http www gnu org copyleft lesser txt Cyto scape also includes a number of other open source libraries which are detailed in the Cytoscape_User_Manu al Acknowledgements below What s New in 2 7 Cytoscape version 2 7 contains several new features plus improvements to the performance and usability of the software Cytoscape User Manual Node Custom Graphics Heal shock cognate 71 kDa Estrogen receptor protein Transcription factor AP 1 isitionalendoplasmic reticulum AlPase Dreast cancer type 1 susceptibility protein Cytoscape User Manual Internally Cytoscape has Custom Graphics API for developers since 2 3 From this version end users can access this feature from standard VizMap GUI You can add up to nine Custom Graphics objects per node Each Custom Graphics object has position Visual Property and you can adjust its position from intuitive GUI Cytoscape User Manual Attribute Functions Data Panel I
21. ID s SS nn iH SM ar Tip Expanding the Network Several of the Cytoscape web services provide additional options in the node context menu To access these options right click on a node and select Use Web Services For example in the screenshot to the right we have loaded the BRCA1 network from IntAct and have chosen to merge this node s neighbors into the existing network Example 2 Retrieving Protein Protein Interaction Net works from NCBI Entrez Gene An entry of NCBI Entrez Gene has a section called Interactions NCBI web service client uses this section to build networks 57 Cytoscape User Manual Select File gt Import Network from web services From the pull down menu select the NCBI Web Service Client e Enter free keywords For example type human muscular dystrophy e Click the Search button Network generated from Entrez Gene data The network above is generated from interaction data matching the keyword human muscular dystrophy Edge color represents data source type BIND BioGRID or HPRD Note since NCBI client extracts interaction data from a huge dataset it takes a long time 30 seconds 5 minutes depends on machine specifications and network connection to import large set of inter actions Example 3 Retrieving Pathways and Networks from Pathway Commons e Select File gt Import gt Network from web services From the pull down menu select the Pathwa
22. Label Position The position of the node label relative to the node Node Label Width The maximum width of the node label If the node label is wider than the specified width Cytoscape will automatically wrap the label on space characters Cytoscape will not hyphenate words meaning that if a single word i e no spaces is longer than maximum width the word will be printed beyond the maximum width Node Tooltip The text of the tooltip that appears when a mouse hovers over the node Node Show Nested Network A boolean value that indicates whether a nested network should be visualized assuming a nested network is present for the specified node Node Size The size of the node Width and height will be equal This visual property is mutually exclusive of Node Height and Node Width Node Height The height of the node Height will be independent of width This visual property is mutually exclusive of Node Size Node Width The width of the node Width will be independent of height This visual property is mutually exclusive of Node Size Node Custom Graphics 1 9 Custom Graphics objects on the node These are selected from Custom Graphics Manager Node Custom Graphics Position I Position of Custom Graphics By default this value is set to center 9 Visual Attributes Associated with Description Edges Edge Label Width The maximum width of the edge label If the edge label is wider than the specified width Cytoscape will automatically
23. Mus musculus NCBIM37 Orthologues Key Attribute Attribute ID HH Data Type M mus Ensembl Gene ID s CR Available attributes H alignments Taxonomy level aln subtype E feature H sap band hsap band feature H sap chromosome name hsap chr name M feature H sap description hsap description M feature H sap display label hsap display label Y feature H sap ensembl gene ID hsap gene stable id E feature H sap ensembl gene ID version hsap gene stable id v a Pi Ld factors UW con ancambl mmm IM frase cnm rino cle le ie Reset Import E e Show the othologs as the list of Ensembl Gene ID on the Data Panel Copy them and use them as the query for IntAct mport Entrez Gene ID from BioMart Use ensembl attribute for the mapping key mport annotations from NCBI The resulting networks looks like the following 65 Cytoscape User Manual 6 Cytoscape Version 268 File Ddt eo Select Layout Plugin Help FF e 4 ee Kel Gy i e026 roba Deskaon Neve Seiten Ex EJ 4 Ei amp 2 BH di Coral Pare ud r Beiuork VWa aeeec F Carre o ee fott Srii HH bel z LESE E53 peter far urna ER Visual Mirna radar sim T Mode View Mapping b hoe abe eh k oe Coh L it Y deos Wa Mapping Missing Trg Dre a bere dnr er T dae Coie dert A he Co arp Fart Cara ior Psp BE thi itg RE A E Tg RELL Auer
24. Networks and Attributes from External Databases Web Service Client Manager Cytoscape 2 6 0 has a new feature called Web Service Client Manager This is a framework to manage various kinds of web service clients in Cytoscape By using web service clients users can access remote data sources easily What is a Web Service A web service is a standardized platform independent mechanism for machines to interact over the network These days many major biological databases publish their data with web service API e List of Biological Web Services http taverna sourceforge net services e Web Services at the EBI http www ebi ac uk Tools webservices This enables developers to write a program to access these services Cytoscape core developer team have developed several sample web service clients using this framework Cytoscape supports many web services including e PSICQUIC Standard web service for biological interaction data sets As of July 2010 the following data providers support PSICQUIC APID e ChEMBL e BioGrid nnateDB e DIP ntAct MatrixDB MPIDB e Reactome e Reactome Fls e MINT iRefIndex e STRING 55 Cytoscape User Manual e Pathway Commons an open source portal providing access to multiple integrated data sets including Reactome IntAct HPRD HumanCyc MINT the MSKCC Cancer Cell Map and the NCI Nature Pathway Interaction database e NCBI Entrez Gene a public database of genes includ
25. NumSigconds lt text gt text cond condZ lt tab gt lt tab gt RATIOS lt tab gt lt tab gt LAMBDAS The first format specifies that both expression ratios and significance values are included in the file The first two text tokens in angled brackets contain names for each gene such as the formal and common gene names The condX token set specifies the names of the experimental conditions these columns will contain ratio values This list of condition names must then be duplicated exactly each spelled the same way and in the same order Optionally a final column with the title NumSigConds may be present If present this column will contain integer values indicating the number of conditions in which each gene had a statistically significant change according to some threshold The second format is similar to the first except that the duplicate column names are omitted and there is no NumSigConds field This format specifies data with ratios but no significance values The third format specifies an MTX header which is a commonly used format Two tab characters precede the RATIOS token This token is followed by a number of tabs equal to the number of conditions followed by the LAMBDAS token This format specifies both ratios and significance values Each line after the first is a data line with the following format FormalGeneName CommonGeneName ratiol ratio2 lambdal lambda2 numSigConds The first two tokens are gene names
26. Shannon P Markiel A Ozier O Baliga NS Wang JT Ramage D Amin N Schwikowski B Ideker T Cytoscape User Manual Cytoscape a software environment for integrated models of biomolecular interaction networks Genome Research 2003 Nov 13 11 2498 504 Launching Cytoscape Cytoscape is a Java application verified to run on Linux Windows and Mac OS X Although not officially supported other UNIX platforms such as Solaris or FreeBSD may run Cytoscape if Java version 5 or later is available for the platform System requirements The system requirements for Cytoscape depend on the size of the networks the user wants to load view and manipulate Small Network Visualization Large Network Analysis Visualization Processor As fast as possible Graphics Card On board Video Highend Graphics Card Monitor XGA 1024X768 Wide or Dual Monitor Getting Started Install Java Memory sm If not already installed on your computer download and install Java SE 5 or 6 Cytoscape 2 5 will no longer run with Java version 1 4 x or lower You must install Java SE 5 or 6 These can be found at Java SE 5 Java SE 6 In general Java SE 6 is faster than 5 If your machine is compatible with the 6 series please try version 6 Install Cytoscape A quick note on upgrading There should really be no issue in upgrading If you have a previous installation you have two options 1 Starting with a clean slate For this you should delete your pr
27. To upper case Convert to upper lower case GO The Attribute Browser has an Attribute Batch Editor This enables you to set and modify attribute values for selected nodes or edges of a specified attr bute at once For example if you want to create a new attribute called Modules and set module names for each group of selected nodes you can use Set command from this editor 47 Cytoscape User Manual Attribute Functions and Equations Attribute Formulas Introduction As of Cytoscape 2 8 attribute values may be formulas A typical example is ABS otherAttrib LOG 10 2 Formulas are modelled after Excel but only support references to other attributes at the same node edge or network Since Cytoscape attribute names may contain embedded spaces optional braces around the attribute name required if the name is not simply a letter followed by one or more letters or digits is allowed e g a name with spaces Backslashes opening braces and dollar signs in attribute names have to be escaped with a leading backslash For example the attribute name ex am p le would have to be written as ex am p le ID is being treated as a pseudo attribute String constants are written with double quotes In order to embed a double quote or a backslash in a string they have to be escaped with a leading backslash therefore the string must be written as Formula results must be compatible with the type of the attribute that they have
28. Unique ID A as source Unique ID B as target and Interactor types as interaction type Then you need to turn off columns used for node attributes Alternative ID A species B etc Other columns can be imported as edge attributes The network import function cannot import node attributes only edge attributes To import node attributes from this table please see the Attributes section of this manual Note 1 This data is taken from the A merged human interactome datasets by Andrew Garrow Yeyejide Adeleye and Guy Warner Unilever Safety and Environmental Assurance Center 12 October 2006 Ac tual data files are available at http www cytoscape org cgi bin moin cgi Data_Sets Basic Operations To import network text Excel tables please follow these steps 1 Select File gt Import Network from Table Text MS Excel 2 Select a table file by clicking on the Select File button 3 Define the interaction parameters by specifying which columns of data contain the Source Interaction Target Interaction and Interaction Type Setting the Interaction Type as Default Interaction will result in all interactions being given the value pp this value can be modified in Advanced Options below 4 Optional Define edge attribute columns if applicable Network table files can have edge attribute columns in addition to network data e Enable Disable Attribute Column By left clicking on a column header in the preview table you can enable
29. YJRO22W YNRO53C pp TRUE abed12 371 1 2344523 YER116C YDL013W pp TRUE abcd12372 1 2342543 YNL307C YALO38W pp FALSE abcd12373 1 2344543 YNL216W YCRO12W pd TRUE abcd12374 1 2344543 YNL216W YGR254W pd IRUE abed1l2375 1 2344543 The network table files should contain at least two columns source nodes and target nodes The interaction type is optional in this format Therefore a minimal network table looks like the following YJRO22W YER116C INLSOTE YNL216W YNL216W XNROSSC YDLO13W YALO38W YCRO12W YGR254W One row in a network table file represents an edge and its edge attributes This means that a network file is considered a combination of network data and edge attributes A table may contain columns that aren t meant to be edge attributes In this case you can choose not to import those columns by clicking on the 27 floating p Cytoscape User Manual column header in the preview window This function is useful when importing a data table like the following 1 Unigue ID A Unigue ID B Alternative ID A Alternative ID B Al 7205 RE TRIP6 PTK2 DL5654 00539731 vv HPRD Currently not aval 4174 ECH fei MCM5 UBA52 P33992 P62987 neighbouring reaction Currently 7040 7040 IGFBI IGFBI PO1137 PO1137 nmr nuclear magnetic resonance Cu This data file 1s a tab delimited text and contains network data interactions edge attributes and node at tributes To import network and edge attributes from this table you need to choose
30. and installation of the library Activ ities other than copying distribution and modification are not covered by this License they are outside its scope The act of running a program using the Library is not restricted and output from such a program is covered only if its contents constitute a work based on the Library independent of the use of the Library in a tool for writing it Whether that is true depends on what the Library does and what the program that uses the Library does 176 Cytoscape User Manual 1 You may copy and distribute verbatim copies of the Library s complete source code as you receive it in any medium provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty keep intact all the notices that refer to this License and to the absence of any warranty and distribute a copy of this License along with the Library You may charge a fee for the physical act of transferring a copy and you may at your option offer warranty protection in exchange for a fee 2 You may modify your copy or copies of the Library or any portion of it thus forming a work based on the Library and copy and distribute such modifications or work under the terms of Section 1 above provided that you also meet all of these conditions a The modified work must itself be a software library b You must cause the files modified to carry prominent notices stating that you changed
31. annotation file and network data are used in this process see the example below Network Data j 7P LIUSYy HU TOLDO I YPLOFSWY pd YELIOTW A J YLROIFW pd YBLIOSW YDRTABC pd Y BL1OBVV YIRDISW YELIDEW I YPL248C pd YBL1OBVV 1 YLROT3V pd Y BL1OBVV 3 YGLDT3C pd Y BL1OBVV 3 YMRIG2C pd Y BL1OBVV YIROT8VW pd Y BL1DOBVV I YPL248C pd YBLT11C 1 YLROT3WW pd YBLTT11C Ontology Data id GO 0005634 z namespaca cellular component 3 det A membrane bounded organelle of eukaryotic cells in which chr 4 subset qaslim generic S subset qaslim oos b subset qaslim plant fisubset qaslim yeast ols a Gi 3731 intracellular membrane bound organelle m Annotation Data Cytoscape User Manual 1731YAP1802 G0 0006897 scD REF ISS YGR241C 101 YAP3 GO 0005634 sco REFIP YHLOOC 101 YAP3 GO 0003700 scD REFIDA F YHLOOC 31 YAP3 GO 0006357 sGD REFIDA P YHLOOSC 157 YAPS5 GO 0005634 scD REF IC GC bziP pssi YIROT8W 157 YAPS GO 0003702 scD REFIDA F bZIP basilYIRO18W 157 YAP5 GO 0000083 scD REFIP P bziP asi YIRO18W 57 YAP5 GO 0045944 scD REFIDA P bZIP basifYIRO18W Mapping Result annotation GO CELLULAR COMPORENT YIRO18W nucleus 5000001457 YAPS transcription factor If you want to map ontology terms onto network objects you need to create a custom annotation file The annotation file should contain at least 2 columns a primary key and an ontology term ID The primary key
32. aru ed Show Mapping Options Show Text File import Options Import everything without checking m siches Gene Association only Annotation File to Ami bie Mapping key Column in Annolation File key Amibe for Network Alias Column Attribute Hamen Dara Type Primary Kay dn Column 1 sl op w0 Column 1 dp String PFI Ontology dp String Annotation File 1a Onielagy Mapping key Column in Annotation File Ontology Column 2 e Protein protein interaction Preview Text File Left Click Enable Disable Column Right Click Edit Column Legend METTI edged ssociation txt Ontology key Attributes Column 1 a PPI Ontoloqy node A Pp node_2 node 1 pp node 2 MI 0445 amp node_2 pp node_3 node 3 pp node_1 MEDDA node 3 pp node 1 node 2 pp node 3 MIEO346 Key Matched 3 First 100 entries are loaded for preview File Size B1 Bytes Import Cancel The basic operation of the Ontology and Annotation Import function is the same as that of the Attribute Table Import The main difference is that you need to specify an additional key for mapping Zeta lo File to Ontology Mapping key Column in Annotation File Ontology Column 2 Protein protein interaction By selecting a column from the Key Column in Annotation File dropdown list you can specify the key for mapping between ontology terms and the annotation file Note When you load Gene Association files Cytoscape uses a speci
33. c Di ae Fund El ced e E 3 LO 333 dH LA Ppa CULE nC ia LAA roga Fe aja ie Fita fend e T We s een mee eu yes Ar Overview Network View 20 Cytoscape User Manual Command Line Arguments Cytoscape recognizes a number of optional command line arguments including run time specification of network files attribute files and session files This is the output generated when the cytoscape is executed with the h or help flag usage java Xmx512M jar cytoscape jar OPTIONS h help Print this message ep yers on Print the version number S session lt file gt Load a cytoscape session cys file Ny network lt Tile gt Load a network file any format e edge attrs lt file gt Load an edge attributes file edge attribute format n node attrrs errle Load a node attributes file node attribute format smy Asmat rx lt file gt Load a node attribute matrix file table fe plugin lt file gt Load a plugin jar file directory of jar files plugin class name or plugin jar URG P props lt i rle Load cytoscape properties file Java properties format or individual property P name value Vi Vizmap EL Les Load vizmap properties file Java properties format Any file specified for an option may be specified as either a path or as a URL For example you can specify a network as a file assuming that myNet sif exists in the current working directory cytoscape sh N myNe
34. disable edge attributes If the header is checked and entries are blue the column will be im ported as an edge attribute For example the table below shows that columns 1 through 3 will be used as network data column 4 will not be imported and columns 5 and 6 will be imported as edge attributes galFiltered csv Column 1 e Column 2 amp Column 3 X n 4 v attr 1 v attr 2 YERO26C YGL122C pp FALSE abcd12345 1 2344543 YGR2 18W YGLOS7W pp TRUE abcd12346 1 2344543 YGLOS W YOR204W pp TRUE abcd12347 1 2344543 YLR249W YPROBOW pp TRUE abcd 12348 12344543 YLR249W YBR118W pp TRUE abcd12349 12344543 YLR293C YGLOS7W pp TRUE abcd12350 1 2344543 YMR146C YDR429C pp TRUE abcd12351 1 2344543 YDR429C YFLO17C pp TRUE abcd12352 1 2344543 YPROROW Y AI 003W nun TRUE ahcd 12353 1 2344 543 28 Cytoscape User Manual e Change Attribute Name and Data Types If you right click on a column header in the preview table you can modify the attribute name and data type For more detail see Modify Attribute Name Type below 5 Click the Import button Import List of Nodes Without Edges Table Import feature supports list of nodes without edges If you select source column only it creates a network without interactions This feature is useful with node expansion function available from some web service clients Please read the section Importing Networks from External Database for more detail Advanced Options Advanced w Show Text File Import Option
35. entire whole and thus to each and every part regardless of who wrote it Thus it is not the intent of this section to claim rights or contest your rights to work written entirely by you rather the intent is to exercise the right to control the distribution of derivative or collective works based on the Library In addition mere aggregation of another work not based on the Library with the Library or with a work based on the Library on a volume of a storage or distribution medium does not bring the other work under the scope of this License 3 You may opt to apply the terms of the ordinary GNU General Public License instead of this License to a given copy of the Library To do this you must alter all the notices that refer to this License so that they refer to the ordinary GNU General Public License version 2 instead of to this License If a newer version than version 2 of the ordinary GNU General Public License has appeared then you can specify that version instead if you wish Do not make any other change in these notices Once this change is made in a given copy it is irreversible for that copy so the ordinary GNU General Public License applies to all subsequent copies and derivative works made from that copy This option is useful when you wish to copy part of the code of the Library into a program that is not a library 4 You may copy and distribute the Library or a portion or derivative of it under Section 2 in object code
36. following is a quick tutorial to learn how to use Gene Name Mapping files Import New ID Sets from BioMart From Cytoscape 2 6 0 you can import various kinds of ID sets from BioMart http www biomart org in dex html BioMart web service client is available as a set of plugins You can install BioMartClient and BioMartUserInterface plugins from Plugin Manager window 157 Cytoscape User Manual 6068 Biomart Web Service Client Query tt ES de d db i ror F AA es Data Source ENSEMBL 48 GENES SANGER Homo sapiens genes NCBI36 Key Attribute Attribute ID H Data Type EntrezGene ID s 5 Available attributes WA feature_page HGNC symbol hgne_symbol Mi feature page Interpro ID interpro ii feature_page PDB ID pdb n Reset Cancel Import 1 Select File gt Import gt Import attributes from Biomart 2 Select a data source For ID mapping select one of the Ensemble Genes data set You need to choose correct species for your network 3 Select Attribute If you want to import new ID sets matching current node IDs select ID 4 Select Data Type This should be the type of ID set selected in Attribute list For example if you select ID for Attribute and your network uses Entrez Gene ID for its node ID you need to select EntrezGene ID s for Data Type 5 Select new ID sets from the list Because BioMart server does not accept query to import lots of annota tions at once y
37. guarantees are made concerning leading or trailing whitespace Object names must be the Node ID or Edge ID as seen in the left most column of the attribute browser if the attribute is to map to anything These names must be reproduced exactly including case or they will not match Edge names are all of the form sourceName edgeType targetName Specifically that is sourceName space openParen edgeType closeParen space targetName Note that tabs are not allowed in edge names Tabs can be used to separate the edge name from the delimiter but not within the edge name itself Also note that this format is different from the specification of interactions in the SIF file format To be explicit a SIF entry for the previous interaction would look like sourceName edgeType targetName Or sourceName whiteSpace edgeType whiteSpace targetName To specify lists of values use the following syntax listAttributeName class java lang String firstObjectName firstValue secondValue thirdValue secondObjectName onlyOneValue This example shows an attr bute whose value is defined as a list of text strings The first object has three strings and thus three elements in its list while the second object has a list with only one element In the case of a list every attribute value uses list syntax 1 e parentheses and each element is of the same class Again the class will be inferred if it 1s not specified in the header line Lists are not
38. internal index of all nodes within the network By default Cytoscape indexes all nodes by the node identifier However you can configure Quick Find to index nodes or edges and you can set any attribute as the index For example if you load up a BioPAX file such as sampleData Apoptosis_BioPAX xml your network will be automatically annotated with numerous attributes To index the network based on cellular location click the Quick Find configuration button and select biopax cellular location from the dropdown list eoe Configure Search Options for Apoptosis Select Index Type ei Index Nodes Index Edges Select Attribute Search on Attribute biopax cellular_location Attribute Description A list of one or more cellular locations e g cytoplasm This attribute should reference a term in the Gene Ontology Cellular Component ontalogy Sample Attribute Values extracellular region plasma membrane mitochondrial outer membrane cytosol mitochondrial intermembrane space Cancel Reindex Network E moe You can then quickly find all proteins located in the plasma membrane by just typing p 134 Cytoscape User Manual BioPAX v 0_5 Tip If you don t know what to search for just leave the search box empty and click on the down arrow directly next to the search box Cytoscape will provide you with an initial list of matches In the case below we will get a list of all distinct cellu
39. lists are not supported Key Attribute for Network o Let dy annotation Taxon dg annotation DB Object Name Ip canonicalNam e 45 Aliases Cytoscape User Manual Cytoscape uses a simple mechanism to manage aliases of objects Both nodes and edges can have aliases If an attribute is loaded as an alias it 1s treated as a special attribute called alias This will be used when mapping attributes If the primary key and key attribute for an object do not match Cytoscape will search for a match between aliases and the key attribute To define an alias column in the attribute table just click on the checkboxes to the left of the column name while importing Alias Column Attribute Name Data Type Column 1 n String Column 2 dp String Column 3 dp String Column 4 b Float Column 5 ES Float Text File Import Options For more detail on these options please see the Import Free Format Table Files section of the user manual in the Creating Networks chapter Attribute Browser i 606 Data Panel EntrezGene ID SGDsymbol Pathway YDR461W 852072 MFA1 KEGG pathway MAPK signali Amino acid residues critical for N te YFLO26W 8505138 STE 2 KEGG pathway MAPK signali N YBRIGOW 852457 CDC28 KEGG pathway Cell cycle y YBR112C 852410 CYC8 KEGG pathway Pathway YCRO84C 850445 TUP1 KEGG pathway YALO40C 851191 CLN3 KEGG pathway O KEGG pathway MAPK signaling
40. na using File gt Import Node attributes This file is shown in part below Probeset YHROSIW probeset2 YHR124W probeset3 YKL181W probeset4 Step 2 After loading the node attribute file select the expression data file sampleData galExp Pvals probeset pvals shown in part below GENE COMMON gal1RG gal4RG gal80R gallRG gal4RG gal80R probeset2 COXO 0 034 0 ll1 0 304 3 757206 01 L 562406 02 7 91340e gt 06 probeset3 NDT80 0 090 0 007 0 348 2 71460e 01 9 64330e 01 3 44760e 01 probeset4 PRSI 0 167 0 233 0 112 6 27120e6 05 7 994006 04 1 44060e 01l 53 Cytoscape User Manual After selecting this file in the field labeled Assign values to nodes using select Probeset You will see that this loads exactly the same expression data as in Case 1 but provides extra flexibility in case the node name cannot be used as an identifier Detailed file format Advanced users In all expression data files any whitespace spaces and or tabs is considered a delimiter between adjacent fields Every line of text is either the header line or contains all the measurements for a particular gene No name conversion is applied to expression data files The names given in the first column of the expression data file should match exactly the names used else where i e in SIF or GML files The first line is a header line with one of the following three header formats lt text gt lt text gt cond cond sx Condi cond sza
41. objects in networks The On tology Server originally called BioDataServer is a Cytoscape feature which allows you to load navigate and assign annotation terms to nodes and edges in a network Cytoscape 2 4 now has an enhanced GUI for loading ontology and associated annotation enabling you to load both local and remote files Ontology and Annotation File Format The standard file formats used in Cytoscape Ontology Server are OBO and Gene Association The GO website details these file formats e Ontologies and Definitions http www geneontology org GO downloads shtml ont e Current Annotations http www geneontology org GO current annotations shtml OBO File An OBO file is the ontology DAG itself This file defines the relationships between ontology terms Cytoscape 2 4 and onwards can load all ontology files written in OBO format The full listing of ontology files are available from the Open Biomedical Ontologies OBO website e OBO Ontology Browser http obo sourceforge net browse html Sample OBO File gene ontology obo http www geneontology org ontology gene ontology edit obo format version 1 2 date 27 11 2006 17 12 saved by midori auto generated by OBO Edit 1 002 subsetdef goslim_generic Generic GO slim subsetdef goslim_goa GOA and proteome slim subsetdef goslim_plant Plant GO slim subsetdef goslim_yeast Yeast GO slim subsetdef gosubset_prok Prokaryotic GO subset default namespace gene_ontolog
42. of gene disease associatio KEGG pathway yndrome 358 ACP 1 Observational study of genotype prevalence i deficiency Blood group 3198 HOKAI Observational study of gene disease associatio brainstem dysgenesis Syr 1482 NEXZ 59 Observational shady of gene disease associato H defect with atricwentricul 2697 GIAI Connmexim amp 3 was absent or decreased in testis KEGG pathway lar septal defecr Hypopl 8517 IKBKG study demonstrates that NEMO is provoked KEGG patmway obacteriosis familial Eer a FAS Ini thyroid glands of patients with Graves diseas lymphopraliferathye syri 355 amp KEGG pathway 4 e Node Attribute Browser Edge Attribute Browser Meteo Right click drag to ZOOM Middle click drag to PAN Welcome to Cytoscape 2 6 0 Use Multiple Services in a Workflow Web services are useful when you combine the result from multiple data sources Example Import and Annotate Networks e Import network from IntAct using keyword In this example type p53 AND species mouse Import Network from Database Data Source IntAct Web Service Client Query p53 AND species mouse Search Property Search Cancel wi e Import human orthologs from BioMart 64 Cytoscape User Manual eoe Biomart Web Service Client d Query bDiossssmart o Data Source ENSEMBL 48 HOMOLOGY SANGER Homo sapiens NCBI36
43. once to select it and then click the Delete button at the bottom of the manager It is best to avoid deleting core plugins as this may cause Cytoscape or other plugins to malfunction A plugin will be completely deleted after you have restarted Cytoscape Update Existing Plugins Going to Plugins Update Plugins will result in Cytoscape automatically accessing the Internet to look for updated versions of the plugins you have installed If newer versions are available Cytoscape will then display the available updates in the Plugin Manager otherwise it will inform you that there are no updatable plugins When multiple updates are detected you will have the option to download some or all of the updates Some updates may require re accepting the license before the download will begin All updates require Cytoscape to be restarted in order for the update to be fully installed After clicking the Update All or Update Selected buttons a progress bar will appear showing the status of the download it will disappear once the update is complete and the Plugin Manager can then be closed by clicking the Close button Note The Update All button will update all listed plugins to the newest available version If you prefer a different version select the name and click Update Selected Download Plugins from a Custom Site The Plugin Manager automatically connects to the Cytoscape website and the sites of registered Cytoscape plugins to check for and down
44. pops up and you can enter the new value for the selected rows Visual Property Dependencies The fourth pane in the Default Editor lists available dependencies that can be established between different visual properties The two that currently exist are Lock Node Width Height and Make Arrow Color Match Edge Color Default Appearance for default K Lech Mode Widt Height Make Amga osos Marc Edge Color Appl 128 Cytoscape User Manual Lock Node Width Height If this menu item is checked Node Width and Node Height mappings are ignored and Node Size overrides them If you want to use Fit node size to label function you need to unlock this Make Arrow Color Match Edge Color If this menu item is checked then Edge Source Arrow Color and Edge Target Arrow Color are overridden and Edge Color is used in both cases Working with Continuous Mapping Editors There are three kinds of Continuous Mapping Editors Each of them are associated with a specific visual attributes Supported Data Type Visual Attributes Color Gradient Editor node edge border label colors Continuous Continuous Editor size width opacity Continuous Discrete Editor All others font shape text Range Setting Panel Range Setting Le J 4 z Min Max Add Delete Each editor has acommon section named Range Setting 1 Handle Value Box This box displays current value for selected slider handle Also you can directly type value in this box to mov
45. supported by the visual mapper and so can t be mapped to visual attributes Newline Feature Sometimes it 1s desirable to for attributes to include linebreaks such as node labels that extend over two lines You can acomplish by inserting into the attribute value For example Cytoscape User Manual newlineAttr YJL157C This is a long nline for a label Import Attribute Table Files As of Cytoscape 2 4 importing delimited text and MS Excel attr bute data tables is now supported Using this functionality users can now easily import data that isn t formatted into Cytoscape node or edge attribute file formats as described above MET Anos Fre O E e Import Attribute from Table Dats Source Air ibutes m Hades Edge Heranrk Input File file cellar usersknnewerkipiceretescapes f build ertaseape v2 d 0 b1 sampleDantagalEspDat penis Calect Fila Fully are Show Advanced Mapping Options Show Text File Import Options Annobalionm File to An ie Mapping Key Cobumn in Annotation File Key Attribute for Network Primary Es p CEHE Alis Column amp tiribute Nam e Data Type gt di canonicalliame GENE dg String CE COMMON n gering galiRG dp String gah RE LA Float gats hp E Clos Vext Pie impor Option Delimiter Preview Oprions s Tab Comme Semicolom Space Other Show al entries in rhe fie wc Shawfirzi 100 enrriez Avuibute Mares Network Import Opliens Transfer first line s atiribune names Star
46. that of the Import Network from Table window 1 Select File Import Attribute from Table text MS Excel 2 Select one of the attribute types from the Attributes radio buttons Cytoscape can import node edge and network attributes 3 Select a data file To load a local file click on the Select File button and choose a data file This can be either a text or Excel xls file To load a remote file type the source URL directly into the text box To show a preview of the remote file click the Reload button on the Show Text File Import Options panel 4 Optional If the table is not properly delimited in the preview panel change the delimiter in the Text File Import Options panel The default delimiter is the tab This step is not necessary for Excel Work books 5 By default the first column is designated as the primary key Change the key column if necessary Annotation File to Attribute Mapping Key Column in Annotation File Primary Key dea GENE 6 Click the Import button Advanced Options Mapping Key Attributes to the primary key Formerly Cytoscape only supported mapping between node edge IDs and the primary keys in attribute files With the introduction of Cytoscape 2 4 this limitation has been removed and now both IDs and at tributes with primitive data types string boolean floating point and integer can be selected as the Key Attribute using the dropdown list provided Complex attributes such as
47. unlocked AND Node Width Height discrete mappings are available you can fit the size of each node to label automatically by selecting this function See the example below a em 1 es b E rund ke 125 resp n 29 De hy Keng i A NW J oil s a e e a a ip YL15 wo 1 BI presen EIN LIE a nl url fi l e i e Ta E k I P Tu proin L31 4A LER bi b no ur nur asl paeme Green LILA LJAA LEE di d U2 anRMP component wg s e E ET CR E Jr ai d e F E N rodea preter S348 hy Pd transcription factor j P ribosomal proben 4244 ui te La a a ee Pg m hada dehydrogenase ATI I 1 Ta s MEM y Jamie ira scrip ion licor a HI A r acdpheiphataae af ee vef por d represor activator protein j ri EH ze e x e p r e i d Tesch m F F pa mm ncm Mee TT ue mruvaze decarboxylase Y paotomal protein LEER ro g i ue L dim 24 A e Z i P 8 1 r i i a j roma Bein LIZA EA eal pgmn LLE SEN UDP glucose 4 en merase pa m r e em nfomal protein 517A pd 1A hd ris di transcriptional regulator n HA Modify Discrete Values Currently this is only for colors You can change overall brightness for discrete color mappings Edit Selected Values at Once You can set multiple values at once First you need to select rows you want to change values then select Edit selected values at once A dialog
48. used to represent compounds and reactions or anything else instead of genes If anetwork of genes or proteins is to be integrated with Gene Ontology GO annotation or gene expression data the gene names must exactly match the names specified in the other data files We strongly encourage naming genes and proteins by their systematic ORF name or standard accession number common names may be displayed on the screen for ease of interpretation so long as these are available to the program in the annotation directory or in a node attribute file Cytoscape ships with all yeast ORF to common name mappings in a synonym table within the annotation directory Other organisms will be supported in the future Why do we recommend using standard gene names All of the external data formats recognized by Cyto scape provide data associated with particular names of particular objects For example a network of protein protein interactions would list the names of the proteins and the attribute and expression data would likewise be indexed by the name of the object The problem is in connecting data from different data sources that don t necessarily use the same name for the same object For example genes are commonly referred to by different names including a formal location on the chromosome identifier and one or more common names that are used by ordinary research ers when talking about that gene Additionally database identifiers from every database whe
49. you can use same VizMap user interface to map Custom Graphics to nodes However before mapping images you need to prepare Custom Graphics in Custom Graphics Manager It is a simple GUI component to add remove images to Cytoscape session Sample icons used in this section is created by Crystal Project distributed under LGPL 107 Cytoscape User Manual Adding New Images to Cytoscape Custom Graphics Manager supports drag and drop for image files and URLs If you want to add images from web browser or local file system you can drag images from them and drop those images to the list of images on the left Add a folder to Custom Graphics Library If you want to add all images in a folder you need to press button on the bottom of the Custom Graphics Manager window Note When you drag and drop images from web browser make sure you are actually dragging URL of the image In some cases images are linked to a HTML page or scripts and in such cases this drag and drop feature may not work Removing Images To remove images from current session s Custom Graphics library simply select graphics from the list and press button Resizing Images You can resize images by typing width height in the text box If Keep Aspect Ratio box is checked width height ratio is always forced to be synchronized Any time you can resize the image to the original size by pressing Original button Use Custom Graphics in VizMap Custom
50. 1 see the Editor chapter for more details 30 Cytoscape User Manual Supported Network File Formats Cytoscape can read network pathway files written in the following formats e Simple interaction file SIF or sif format Nested network format NNF or nnf format e Graph Markup Language GML or gml format XGMML extensible graph markup and modelling language e SBML BioPAX e PSI MI Level 1 and 2 5 e Delimited text Excel Workbook xls The SIF format specifies nodes and interactions only while other formats store additional information about network layout and allow network data exchange with a variety of other network programs and data sources Typically SIF files are used to import interactions when building a network for the first time since they are easy to create in a text editor or spreadsheet Once the interactions have been loaded and network layout has been performed the network may be saved to GML or XGMML format for interaction with other systems All file types listed except Excel are text files and you can edit and view them in a regular text editor SIF Format The simple interaction format is convenient for building a graph from a list of interactions It also makes it easy to combine different interaction sets into a larger network or add new interactions to an existing data set The main disadvantage is that this format does not include any layout information forcing Cyto scape to re compute
51. 10 Apply Force Directed layout Final view of the window looks like the following 121 Cytoscape User Manual EE Cytoscape Desktop New Session SHQQRQQR 8 d ii Control Panel Wu eno galFiltered sif Network MizManper Editor b Curremr Visaal Style default m Wi Detaults Visual Mapping Browser 5i fn m T Node Visual Mapping T Node Sze Degree Mapaing Type Discrete Mapping 10 0 a 45 0 3 60 0 4 75 0 5 30 0 B 105 0 7 120 0 B 135 0 y 150 0 11 155 0 17 180 0 T Welcome to Lytoscape 2 5 Hsghnt click drag te ULIM Middla clitk drag to PAN Tutorial 5 Using Custom Graphics in Visual Styles This tutorial is a quick introduction to new Custom Graphics feature in Cytoscape 2 8 0 1 Prepare images This can be any type of bitmap graphics but in this tutorial we are going to use Crystal Project s PNG icons You can download it from here 2 Start Cytoscape and select View Open Custom Graphics Manager 3 Click button and select an image folder 4 All images in the folder should appear in the Custom Graphics Manager 122 Cytoscape User Manual Cusiom Graphics Manager 5 Load a network and apply Degree Sorted Circle Layout This creates new integer node attribute Degree 6 Click VizMapper tab in the Control Panel and select Solid style 7 Click default view to open Default Appearance Editor 8 Click NODE CUSTOM GRAPHICS 41 and select any of a custom graphics f
52. 71 NP NE Cytoscape User Manual Note that line wrapping has occurred here each line in this example starts with the letters SP See the README file for more information ftp ftp ebi ac uk pub databases GO goa HHUMAN README Finally run the script to create your three annotation files for human proteins bioproc anno GO biological process annotation e molfunc anno GO molecular function annotation cellcomp anno GO cellular component annotation using the supplied python script It may be necessary to modify this script slightly if RefSeq identifiers are not used as canonical names or if you are using a more recent version of Python python parseAssignmentsToFlatFileFromGoaProject py gene association goa human xref See below for Python script listing Python script examples These scripts as described above require Python version 2 2 or later Script 1 parseGoTermsToFlatFile py f parseGoTermToFlatFile py translate a GO XML ontology file into a simpler Cytoscape flat file RECESS SRev s on 1438 Darter 20027057 LS 00236643 e import re pre sys def flatFilePrint id name isaIDs partofIDs isa YE bem Ve Ets gt 1033 isa isa for Salon ee Ee isa isaID isa isa partof LE Len PpartotiDs 2 0 partof partof for partorLlb xn partotibs partof partofID Parto pe t4 partot t result enp np s np S np s np np s np np s n
53. AA PDA WE LA Pm A AA PAPA PDA YE So PPAL Fa morgan Y EE CX pa a Cactus Dor2 on abo am mue ri cer EBEN TEY dE SPIEL Bs im 551 haud esl Rios Deer Mipir eo a ul ty 6t a ee ida i gat Farm cc STI dude oe Die LE vun pe pnr e room EEDD pala Ai dom IA LD o dl Var of Geo dag dee irn Barre RADA Frodo RA hingga E cold cere REGS pate Bisrgicze cancer Arad E AG bona ady cf gane Da pube razas cancer pario Bey bo IDA reih he Li TEX 1 Sr prece Bt L eos i Pod Ve et ara dihi dido prometi Zen E a qnc ee paate o FC inig e RICO partea Del nace ICE Ra tora Voie of per dadas ann n haul TuS li Hee Bee Va of erg dd ee reais anger Bear IDA reit eo Going Re M PREC antike ME Bow A d m seriada palsy ae Are Be clea ery eeng CA rr tates marcwcooy EN Bx EICH pathy Cee mop wucema Esg Cerca pond 1 Of gera era oer Lex ami prp Benger Le era qo crane Hex KI CA Safe Arie r poen r Pao rada negulaten dl AA A a eee ee A a H Wen Ti rond ieu Kess Pasa PRED parar Ue STAT tabag puta E Foy Pas 8 rode im tee repo ol MC p Pd gar Teil KE CX pathagy Beret ic opera Great Rass page rt moWwpbgar mara py afi ll KS Ch A L Apiuni dol LO A 156003 ae Brea Cancer e Baal emid fen se 07 ase KE og para Lee dey igation Ras ate sapori Cat fw eat ua a D ieren re D Colorectal cancer Dama ARA Viele ER Ca potted Aeon gods DOGO parry Tar Sain p tel peepee Hepatocellular carcinoma 5 e rare biegpeg OOOO Byar Ta oan E
54. Cytoscape is running Cytoscape Preferences Managing Properties Important If you have used previous versions of Cytoscape you will notice that handling of properties has changed The most important change is that properties are no longer saved by default to the current directory or to your home cytoscape directory Properties are stored by default in Cytoscape session files cys extension The cytoscape props file still exists in the cytoscape directory but is only written to when the user explicitly requests that the current settings be made the defaults for all future sessions of Cytoscape Unless you have something important in your cytoscape cytoscape props file your best bet will be to delete the file and use the defaults The Cytoscape Properties editor accessed via Edit Preferences Properties is used to specify general and default properties Properties are now stored in Cytoscape session files so changes to general properties will be saved as part of the current session but will only carry over to subsequent sessions if they are set as defaults or exported using the File Export function Cytoscape properties are configurable via Add Modify and Delete operations 22 Cytoscape User Manual 3 Cytoscape Preferences Editor Properties Froperty Name bioDataServer Pleasespecify canonicalizeNames true cytoscape version num 2 5 defaultSpeciesName Saccharomyces cerevisiae defaultVisualst
55. D YKRO97W YMLOS1W YNL167C YPLOSSC YOLOSSW YJL157C YKL109W YJL159W YOLOS6C YIL143C YIL133C YNL117W YPL248C Li L O Oo Degree 4142135623730951 4142135523 30951 4142135623730951 A 4142135623730951 4142135623730951 4142135623730951 4142135623730951 315524 903554 2 4 2 2 2 4 4 2 d 2 2 1 3 bel la bel a bel jl jl Pl eet pet P YALOSSW 7320508075688772 Node Attribute Browser Edge Attribute Browser Attribute values can now be spreadsheet like formulas In particular an attribute on a node edge can refer ence other attributes on the same node edge About 40 built in functions have been provided and it is rel atively easy to implement a Cytoscape plug in of your own to add additional functions An example plug in can be found with the other plug in tutorials Arbitrarily complex arithmetic string and logical boolean D tons are supported as well as limited list construction The syntax closely follows that of Microsoft Excel Other New Features and Bug Fixes e Plugin search you can now search plugins by keyword s e Many many bug fixes Please Cite Cytoscape Cytoscape is anon profit open source project To help make the Cytoscape project sustainable your support is essential Since Cytoscape project depends on government private grants citation is the most important support for us When you publish papers books posters please cite the following paper
56. Data into Cytoscape The easiest way to make annotations available to Cytoscape is by loading annotations into the Cytoscape annotation server This is the default behavior for the official release of Cytoscape The Annotation Manifest You must first create a text file to specify the files you want Cytoscape to load Here is an example from a file which for convenience we usually call manifest ontology goOntology txt annotation yeastBiologicalProcess txt annotation yeastMolecularFunction txt annotation yeastCellularComponent txt Use the Cytoscape b command line argument to specify the annotation manifest file to read e g b manifest Please note that the s switch which sets the default species for your data is required to exactly match the species named in any annotation file you wish to use Getting and Reformatting GO Data The Gene Ontology GO project is a valuable source of annotation for the genes of many organisms In this section we will explain how to 1 Obtain the GO ontology file 2 Reformat it into the simpler flat file Cytoscape uses 3 Obtain an annotation file we illustrate with yeast and human annotation 4 Reformat the annotation files into the simple Cytoscape format Obtain the GO ontology file Go to the GO XML FTP ftp ftp geneontology org pub go xml page Download the latest go Y YY YMM termdb xml gz file Reformat GO XML ontology file into a flat file gunzip go YYYYMM termdb xml gz pyt
57. EES Editor H P AAA A A AAA A ament Visus JO i AA A AAA d 4 d AA d A GA A A AAA A AA AA A Tutorial VS1 m ud A h ae ACA ASA A A acra ahh Dufauits D ew a m E ok amp SA Ab A kA ue SAA SA AA A tk ASA AAA A dd AA A A A A A NSA KS i a SA A A wis ual Mapping Srewser k k a a e KA ad e A A ee cd 45mm Ae MR ee rar A AA h A gc rm nl A Edge Color Couble Chck bo cre KA PE n A 2 X A5 Edge Fora Face Double Chick po cri A A WA Ak A AAA A En Chae ee ce lie Edge Fort Sg Deus Check bo cre ff A A hh aa hk A KA WA 4 4 A A Edge Lahr Deoupk Chick lo cre A A 4 ASA AAA A Edge Label Color Ooubie Clck to cre AAA 4 4 4 4 4 4 4 Edge Label Opacity Doud irk to cre Edge Line She DoubleClick im cre Data Pare ral Edge Line Width Double ick p cre bad 1d Ej 1 x Edge Opacity Double Click m cre E Je Edge South Aer e Edge Source Are ice arre Arrow Welcome to Cytoscape 2 5 Diui Check ns cre Douala Check pn cre fraile e i rre 3 Right click drag to ZOOM Nede Attribute Browser Edge Attribute Browser 114 Middle click drag to PAN Bewark Artibute Breas Cytos
58. ILES esas adas 81 Waa saN TaS ad de celo 81 Introduction to the VizMapper User Interface nenne aa 96 Introduction fo Visual SES at ida 97 Visual Attributes Graph Attributes and Visual Mappers ences eeeeeeeseneeaeneeas 99 CustomyGraphics Wana rr Eege ger 107 Misual Styles re e DEE 111 Advanced TOPICS asian 126 Manas ne Visual SEV TeS tii ii AN 131 Bypassino Visuales uenientem eee le Sedo Ett tatcm Oud pelos uobis tls ege 131 Firiding and Pilterins Nodes and Ess aeg a ebbe eal ue aot Y ae 132 Quick indes see abc ec or ie te ESO ceti kc Sc ca i toes 132 Filters M RET RT T QE 136 EE 137 Us Old Piliets ati ea A talea AA AA AE 141 Whe Select MECH ses rel 145 Editi Networks nase oad tiene nifi a ai 146 Add Interactions CSTE Sia ll das 147 Nested NEW OS unm SS AE A SI A SN A E tears atu oa ond aue el ted 148 Introducino Nested NetWork S a iia 148 Creatine NESEUNEIWOLKS isa dla diario 148 Nisdalisatiomor Nested Nelworks ind 148 Programmatically Manipulating Nested Network 148 Plugins and the Plubtm Manag er et a A a 148 The E Er E ne een erh seele 148 GEENEN A CIN Zeiss nee reg 149 Delete Existe IPIUPIBS ses a ae 150 Update bxiseme Pl een 150 Download Plugins from 4 Custom Site an en a u ea tes 150 CONGO an EE 150 What ate CAOBA SAR SSA AE AAA A 150 Basic USE sola 152 R nderimo EAS ME ii a 152 What 1s bevel Of Detar EOD A SA eod EHE Lo bu d etd 152 ADNOG Renee 153 Ontology and Annotation File Format u a a ee E bes
59. LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER OR ANY OTHER PARTY WHO MAY MODIFY AND OR RE DISTRIBUTE THE LIBRARY AS PERMITTED ABOVE BE LIABLE TO YOU FOR DAMAGES INCLUDING ANY GENERAL SPECIAL INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE LIBRARY INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE LIBRARY TO OPERATE WITH ANY OTHER SOFTWARE EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POS SIBILITY OF SUCH DAMAGES END OF TERMS AND CONDITIONS 180 Cytoscape User Manual Appendix C Increasing memory for Cytoscape How to increase memory for Cytoscape from Notes on memory consumption Cytoscape User Manual For users interested in loading large networks the amount of memory needed by Cytoscape will increase Memory usage depends on both number of network objects nodes edges and the number of attributes Here are some rough suggestions for memory allocation Suggested Memory Size Without View Number of Objects nodes edges Suggested Memory Size 0 70 000 512M default 70 000 150 000 800M Suggested Memory Size With View Number of Objects nodes edges Suggested Memory Size 0 20 000 512M default 20 000 70 000 SOOM Changing memory allocations on Windows Mac and Linux machines There are a number of ways to change Cytoscape s memory allocation dependi
60. ML file directly Once a network is built in SIF format and then laid out the layout is preserved by saving to and loading from GML Visual attributes specified in a GML file will result in a new visual style named Filename style when that GML file is loaded XGMML Format XGMML is the XML evolution of GML and is based on the GML definition In addition to network data XGMML contains node edge network attributes The XGMML file format specification 1s available at http www cs rpi edu puninj XGMML 38 Cytoscape User Manual XGMML is now preferred to GML because it offers the flexibility associated with all XML document types If you re unsure about which to use choose XGMML 2 7 note There is a java system property cytoscape xgmml repair bare ampersands that can be set to true if you have experience trouble reading older files This should only be used when an XGMML file or session cannot be read due improperly encoded am persands as it slows down the reading process but this is still preferable to attempting to such files using manual editing SBML Systems Biology Markup Language Format The Systems Biology Markup Language SBML is an XML format to describe biochemical networks SBML file format specification is available at http sbml org documents BioPAX Biological PAthways eXchange Format BioPAX is an OWL Web Ontology Language document designed to exchange biological pathways data The complete set of
61. Manper Editor lb N Curremr Visaal Style hd De Defaults Visual Mapping Browser 5i fn m Mode Visual Map E mode Label L F Unused Properties Hode Color Hode Border Color Node Shape Node Sine Node Width Node pitii Node Font Face Hode Font Size Node Label Calo Node Tooltip Node Label Position Welcomes bo Lytoscape 2 5 Highnt click drag te ULIM Middla clitk drag to PAN 6 Cretate a Discrete Node Color Mapping Select Degree as controlling attribute 7 Select Node Color then right click to show popup menu Select Generate discrete values gt Rainbow 1 It generates different colors for different attribute values as shown below 120 Cytoscape User Manual m8 Cytoscape Desktop New Session SE LJ Q e EX amp E a Wl Corirol Para LT ana galFiltered sif Ll Network VizManper Editor lb N Curremr Visaal Style default Gel Defaults Visual Mapping Browser 5 50 um T Node Wisual Mapping Mode Color Degree Wapping Type Daire Mappra l es d 1 3 CH 4 5 LH 6 I 7 gt B a 5 ECH 11 EA 17 DERE 7 r Welcome to Lytoscape 2 5 Hsghnt click drag te 200M Middla clitk drag to PAN 8 Cretate a Discrete Node Size Mapping Select Degree as controlling attribute 9 Select Node Size and right click to show popup menu Select Generate Discrete Values Series Numbers Only Type 30 for the first value and click OK Enter 75 for increment
62. Menus File The File menu contains most basic file functionality File Open for opening a Cytoscape session file File New for creating a new network either blank for editing or from an existing network File Save for saving a session file File Import for importing data such as networks and attributes and File gt Export for exporting data and images Also File Print allows printing while File Quit closes all windows of Cytoscape and exits the program Edit View 51 New gt Open SE Save ge Save As 05 Import p Export gt Print AP Quit Q Edit The Edit menu contains Undo and Redo functions which undo and redo edits made in the Attribute Browser the Network Editor and to layout There are also options for creating and destroying views graphical representations of a network and net works the raw network data not yet visualized as well as an option for deleting selected nodes and 15 Cytoscape User Manual edges from the current network All deleted nodes and edges can be restored to the network via Edit gt Undo Editing preferences for properties and plugins is found under Edit Preferences Properties View Select Layout Plugins Undo Move 7 Redo Y Create View XV Destroy View W Destroy Network LW Delete Selected Nodes and Edges D Preferences View The View menu allows you to display or hide the network management pan
63. O PF03952 PF00113 A THROS3C YHRO53C 856450 85 CUP1 1 1AOO 140 0 Edge Attribute Browser Network Attribute Browser 62 Cytoscape User Manual Example 2 Import Annotations from NCBI Entrez Gene Database NCBI Entrez Gene Data Source Key Attribute Attribute ID Data Type Entrez Geni Available Annotation Category x Summary Ka Publications Mi Phenotypes B Pathways I General Protein Information A Additional Links Mi Gene Ontology Reset Cancel Import NCBI Entrez Gene database can be used as network data source and annotation repository You can use NCBI web service client to import gene annotations from Entrez Gene e File gt Import gt Import attributes from NCBI Entrez Gene Data Source is fixed to NCBI Entrez Gene Data Type is also fixed to Entrez Gene ID This means Cytoscape attribute selected in Attribute list should be Entrez Gene ID Select Annotation Category If you select a category all of the annotation under the category will be imported 1 e multiple Cytoscape attributes will be created for each category Press Import The following is a sample human network RUAL subset sif annotated by NCBI client 63 Cytoscape User Manual Boe Cytoscape Desktop New Session eoe RUAL subset sif CAII See SEN ye FE o A BR Too AA Kms wed oc Se es i LX ceres XO EES A eae pet e o ORT s do o 2h De TR NT ERBE AT MM Data Panel
64. S protein kinase subunit Saccharomyces cerevisiae YALOUASW translation elonga EF 1 beta translation elongation fa Saccharomyces cerevisiae YBROSOC Glc7p regulatory Glc7p regulatory subunit Saccharomyces cerevisiae YBROASC LPL Glc7p regul Glc p regulatory subunit Saccharomyces cerevisiae YOR178C GAC Glc7p reg Glc p regulatory subunit Saccharomyces cerevisiae Nade Attribute Browser Edge Attribute Browser Network Attribute Browser Note that CytoPanel 2 now has a Dock Window control If you select this control the window will dock onto the main window Cytoscape also has an editor that enables you to build and modify networks interactively by dragging and dropping nodes and edges from a palette onto the main network view window The Node shapes and Edge arrows on the palette are defined by the currently used Visual Style To edit a network just select the Ed itor tab on CytoPanel 1 An example of an editor with the palette contained in CytoPanel 1 and defined by the BioMoleculeEditor Visual Style is shown below 14 Cytoscape User Manual e ee Cytoscape Desktop New Session BARAR DOR Er Control Panel Tal P0 0 Sample Network 1 y Network VizMapper Editor Directed Edge kb Add a Node Ma at Data Panel CL SLi Je ID camanicall arme nodes node a Node Attribute Browser Edge Attribute Browser d Network Attribute Browser Welcome to Cytoscape 2 5 Right click drag to ZOOM Middle click drag to PAM The
65. SGD REF SOOO 3642 PSI DEG 2619 ei i eed SCD 5000007287 155_RAMA 0009715 SGD REFISQUO073642 FMIDx62619 YPRIOZC SCD 000007287 155 RRMA 600042255 SGO REFISODODS 1605 PMID 2 1674 YPR110C SCH 5000007287 155 RRAA 600043037 SGD REF SDOO073643 PMITE62801 E very LW 550 40000073 FER AIS RAMA CDOTS COREFF 50000733 72 PMID 67 S FR YPR119W 560 5000007 IEA AUS BRA npenons23s SGD REF SODOQODZ X372 Fil Des 5 3 l l SCD 00000 728 715 RRNA 0001735 GD REF S00007 3372 PIE 7538 YPR124W SCH 215 RRMA COOO2255 SGD REF 5000073372 P MID 67558 YPR145W rr ra a DS mal mm mem nam m mi AAA PT er d PRLATC gara oca t a Heber of maiched Primary Key and Kay breng pair Etat 100 arririaz are kaded Tor preira Fite Sipe Untreoen Pero Dara Sauce Cytoscape 2 4 provides a graphical user interface to import both ontology and annotation files at the same time Import Gene Ontology and Gene Association Files For convenience Cytoscape has a list of URLs for commonly used ontology data and a complete set of Gene Association files To import Gene Ontology and Gene Association files for the loaded networks please follow these steps Important All data sources in the preset list are remote URLs meaning a network connection is required Step 1 Select an Annotation File Annotation Q Gene Association file for Saccharomyces cerevisiae Please select an annotation data source
66. The names in the first column are the keys used for node name lookup these names should be the same as the names used elsewhere in Cytoscape i e in the SIF GML or XGMML files Traditionally in the gene expression microarray community who defined these file formats the first token is expected to be the formal name of the gene in systems where there is a formal naming scheme for genes while the second is expected to be a synonym for the gene commonly used by biologists although Cytoscape does not make use of the common name column The next columns contain floating point values for the ratios followed by columns with the significance values if specified by the header line The final column if specified by the header line should contain an integer giving the number of significant conditions for that gene Missing values are not allowed and will confuse the parser For example using two consecutive tabs to indicate a missing value will not work the parser will regard both tabs as a single delimiter and be unable to parse the line correctly Optionally the last line of the file may be a special footer line with the following format NumSigGenes intl int2 54 Cytoscape User Manual This line specified the number of genes that were significantly differentially expressed in each condition The first text token must be spelled exactly as shown the rest of the line should contain one integer value for each experimental condition Importing
67. YMRO43W 855060 MCM1 KEGG pathway aa YER111C 856847 SWI4 KEGG pathway 1 YNLO36W 855692 NCE103 CEET LUZ TONCEMIramons are rer Am a es mr mm cm Edge Attribute Browser Network Attribute Browser When Cytoscape is started the Attribute Browser appears in the bottom CytoPanel This browser can be hidden and restored using the F5 key or the View gt Show Hide attribute browser menu option Like other CytoPanels the browser can be undocked by pressing the little icon in the browser s top right corner To swap between displaying node edge and network attributes use the tabs on the bottom of the panel labeled Node Attribute Browser Edge Attribute Browser and Network Attribute Browser The at tribute browser displays attributes belonging to selected nodes and or edges and the currently selected network To populate the browser with rows as pictured above simply select nodes and or edges in a loaded network By default only the ID of nodes and edges is shown To display more than just the ID click t h e Select Attributes E button and choose the attributes that are to be displayed select various attributes by clicking on them and 46 Cytoscape User Manual then click elsewhere on the screen to close the attribute list Each attribute chosen will result in one column in the attribute browser Most attribute values can be edited by double clicking an attribute cell only the ID cannot be edited Newline
68. a license from the original licensor to copy distribute link with or modify the Library subject to these terms and conditions You may not impose any further restrictions on the recipients exercise of the rights granted herein You are not responsible for enforcing compliance by third parties with this License 11 If as a consequence of a court judgment or allegation of patent infringement or for any other reason not limited to patent issues conditions are imposed on you whether by court order agreement or other wise that contradict the conditions of this License they do not excuse you from the conditions of this Li cense If you cannot distribute so as to satisfy simultaneously your obligations under this License and any other pertinent obligations then as a consequence you may not distribute the Library at all For example if a patent license would not permit royalty free redistribution of the Library by all those who receive copies directly or indirectly through you then the only way you could satisfy both it and this License would be to refrain entirely from distribution of the Library If any portion of this section 1s held invalid or unen forceable under any particular circumstance the balance of the section is intended to apply and the section as a whole is intended to apply in other circumstances It is not the purpose of this section to induce you to infringe any patents or other property right claims or to contest validity of any s
69. a new layout of the network each time it 1s loaded Lines in the SIF file specify a source node a relationship type or edge type and one or more target nodes nodeA relationship type nodeB nodeC relationship type nodeA nodeD relationship type nodeE nodeF nodeB nodeG nodeY relationship type nodeZ A more specific example is nodel typeA node2 node2 typeB node3 node4 noded node0O The first line identifies two nodes called nodel and node2 and a single relationship between nodel and node2 of type typeA The second line specifies three new nodes node3 node4 and node5 here node2 refers to the same node as in the first line The second line also specifies three relationships all of type 3l Cytoscape User Manual typeB and with node2 as the source with node3 node4 and node5 as the targets This second form is simply shorthand for specifying multiple relationships of the same type with the same source node The third line indicates how to specify a node that has no relationships with other nodes This form is not needed for nodes that do have relationships since the specification of the relationship implicitly identifies the nodes as well Duplicate entries are ignored Multiple edges between the same nodes must have different edge types For example the following specifies two edges between the same pair of nodes one of type xx and one of type yy nodel xx node2 nodel xx node2 nodel yy node2 Edges c
70. abases 5U088 ENSC Reactome dd ZACES A2WDG4 AZVDGS 059HF4 OFSPK ENSC 4 15141 015208 Q98WI3 014747 ENSG Ensembl Gene View PIR 94846 QGPJKS GENERT ENSG Other Biological DB Ded te ve Model Organism DB 60298 QSWUY7 Q9UKDS Q9UKD9 QIUKE msc Pntology ato tha MOREA TEAGEC ANAT AMARA ki ak Acknowledgements Cytoscape is built with a number of open source third party Java libraries The Cytoscape team gratefully acknowledges the following libraries The Colt Distribution Open Source Libraries for High Performance Scientific and Technical Computing in Java Information is available at http hoschek home cern ch hoschek colt Graph INterface librarY a k a GINY Information is available at http csbi sourceforge net e JDOM Information is available at http www jdom org JUnit Information is available at http junit org JGoodies Looks Information is available at http www jgoodies com freeware looks index html e Piccolo Information is available at http www cs umd edu hcil jazz Type Specific Collections Library from Sosnoski Software Solutions Inc Information is available at http www sosnoski com opensrc tclib e Xerces Java XML parser Information is available at http xml apache org xerces y 167 Cytoscape User Manual e CLI command line parser Information is available at http jakarta apache org commons cli FreeHEP library Information is available
71. al loader program designed only for Gene Association files Because of this program all attributes will be named automatically Also ontology IDs will be converted into term names and NCBI taxonomy ID will be converted into actual species name However for custom annotation files those processes will not be applied All ontology terms will be mapped as term IDs Linkout LinkOut provides a mechanism to link nodes and edges to external web resources within Cytoscape Right clicking on a node or edge in Cytoscape view opens a popup menu with a list of web links 165 Cytoscape User Manual The external links are specified in a linkout props file which is included in the cytoscape jar file The defaults include a number of links such as Entrez SGD 1HOP and Google as well as a number of species specific links In addition to the default links users can customize the LinkOut menu by adding or removing links by editing the linkout properties found under Edit Preferences Properties External links are listed as key value pairs in the Linkout props file where key specifies the name of the link and value is the search URL The LinkOut menus are organized in a hierarchical structure that is specified in the key Linkout key terms specific for nodes start with the keyword nodelinkouturl for edges this is edgelinkouturl For example the following entry nodelinkouturl Model Organism DB SGD yeast http db yeas
72. al visual properties size opacity To change the value assigned on Y axis visual property shown in the example above is node size drag the red squares or double click on the squares to directly type exact value Continuous Discrete Editor i 606 Continuous Editor for Node Shape Continuous Mapping for Node Shape v 7 Min 2 426 1 00000 1 00000 j gallRGexp Max 2 058 Range Setting of Add Delete E Continuous Discrete Editor is used to create mapping from numerical attribute values to discrete visual properties such as font shape or line style To edit a value for specific region double click on the icon on the track 130 Cytoscape User Manual Managing Visual Styles All Cytoscape Visual Style settings are initially loaded from a a default file called vizmap props that cannot be altered by users When users make changes to the visual properties a vizmap props file is saved in the session file This means that assuming you save your session you will not lose your visual properties No other vizmap props files are saved during normal operation Saving Visual Styles Visual styles are automatically saved with the session they were created in Before Cytoscape exits you will be prompted to make sure you save the session before quitting It is also possible to save your visual styles in a file separate from the session file To do this navigate to the File Export Vizmap Property Fil
73. alMame YC Mode canonicalMame Node null 0 0 within distance NodeTopology that pass the Filter Select All Filter iv Apply selected Filter The node topology filter allows you to select all nodes selected by a preexisting filter and having n neigh bours found at a distance of m or fewer edges away For instance to select all the nodes adjacent to a node with the canonical name matching YD you would select nodes with 1 neighbors within distance 1 that pass the filter Node canonicalName YD The node topology filter depends on the existence of other filters By default No Filter is selected it doesn t filter out anything but rather selects all nodes 144 Cytoscape User Manual Boolean Filter Use Filters Manage Filters Boolean Meta Filter Create new Filter Remove selected Filter _ Filter Mame BooleanMeta Available Filters Select objects that pass ALL v of the selected Filters Select All Filter Select All Filter Mode canonicalldame YL Mode canonicalName YL Mode canonicalName YC Mode canonicalName Yc Mode canonicalName Mode canonicalName Node null 0 0 Node null 0 0 ModeTopology ModeTopology BooleanMeta BooleanMeta Apply selected filter Negate
74. ames in the text file as attributes Fer Cytoscape Desktop Hew Session File Eda View Select Layout Plugins Help GH aaa Y Ae el Control Panel so E RUALsubseLsif Jg Network vizMapper Fiters Hetwork Hodes Scott LI 419180 ioga auia BHIF 3 554 ECL2 adenovirus EIS I9kD inti zuMo2 5513 HSMT2 M GCELI7 1391 SHTX h zuMoz 6612 SMT homolog 1 SHTI suppr sus 164754 FL 1060 MCC104224 MY SCTA 544 SCT SCTA Vpu binding prot SCK 6446 SCK SCH L Serine ihreonine g ELMH Nowe Altribute Browser j Edge Altribute Browser Network Attribute Browser Fi Welcome to Cytoscape 2 5 Right cEck drag to 00M Middie click drag to PAM lt listitem gt At this point nodes have multiple names including HGNC UniProt and EntrezGene ID You can import other attribute files using these keys These imported names IDs are useful when you import GO An notation 160 Cytoscape User Manual Import Ontology and Annotation Min omae Dar arme most Import Ontology and Annotation uma Srestcet Ani ibe Amot ation lad Gene Asspriatian file Tar arca ro Cece el ae Ontology had Gene Ontology fam Al au ed naa dented Mappieg Qpranr Show Test Fie impor Optlans Previa 21 Gene Association Len Click Edit Column Right Click ON OFF Columr Legend METTRE CEET Key Artibai v DB wv IR Obec ID wv DE_Objet_Symbol v Qualifier Gold DEReference DIM 550 GMO 3 R7 155 BRA miir
75. are detailed below QAQA From Left to Right e Zoom Out Zoom In Zoom Selected Region Zoom Out to Display all of Current Network 66 Cytoscape User Manual You can also zoom in out by holding down the right mouse button and moving the mouse to the right zoom in or left zoom out Pan You can pan the network image by holding down the middle mouse button and moving the mouse You can also pan the image by holding down the left mouse button over the blue box in the Network Overview panel in the lower left hand of the Cytoscape desktop Other Mouse Behaviors Select Click the left mouse button on a node or edge to select that object You can hold down the Shift key to select more than one node edge or you can hold down the left mouse button and drag the mouse to select groups of nodes edges Context Click the right mouse button on a node edge to launch a context sensitive menu with additional information about the node edge Node Context Menu This menu can change based on the current context Typically it shows e Visual Mapping Bypass Nested Network Use Web Services e LinkOut Nested Network Node Context Submenu e Set Nested Network Let s the user select any network in Cytoscape as the current nodes nested network If the current node already has a nested network it will be replaced e Delete Nested Network After being selected the current node will no longer have a nested network associated wi
76. ars on the network Nested Networks Introducing Nested Networks As of version 2 7 Cytoscape gained the ability to associate a nested network with a node Such a nested network is not the network that the node is contained in but any other network currently defined in Cytoscape This capability allows for creation of network hierarchies as well as circular relationships For example various module finding plugins make use of nested networks in the overview network that they generate There each node representing a module contains a nested network Creating Nested Networks There are currently two ways in which a user can create nested networks 1 By importing a Nested Network Format NNF file See Network_Formats NNF 2 By manually constructing networks and assigning nested networks to individual nodes through the right click node context menu See Navigation_Layout Nested Network Node Context Submenu Visualisation of Nested Networks Nodes containing nested networks that are zoomed in sufficiently display an image for the nested network If no current network view exists for the nested network the image will be a default icon otherwise it will be a low resolution rendering of the nested network s current layout Programmatically Manipulating Nested Networks The giny model node interface defines two methods e public void setNestedNetwork final GraphPerspective graphPerspective This will assign a network GraphPersp
77. artotiDs for ref in m4 partoflDs append ref flatFilePrint id name isalDs partofIDs else badElements 1 print gt gt Sye sctderc no match Co Masra prin So sys slderc eee NAnenpess e npessWi np Print gt gt SyS SUtdaerr goodElements np np d np np goodElements print gt gt sys stderr badElements np np d np np badElements Script 2 parseAssignmentsToFlatFileFromGoaProject py Tmport SVs def fixCanonicalName rawName for instance trim YBRO85W ANC3 to YBROS85W bar rawName find TE bar 9v return rawName return rawName bar def fixGoID rawID bar xawIb rtrznd s y wl 173 Cytoscape User Manual return rawID bars def readGoaXrefFile filename lines open filename read split n result tox rne qm J nes LE ken ine lt 107 continue tokens ILine sSplit CET ipi tokens 2 np tokens 5 semicolon np find if semicolon gt 0 np np semicolon if len ipi gt 0 and len np gt 0 result ipi np return result GE oM Qr P FR if len sys argv 3 print error parse gene associations file from GO goa xrefs file gt sys exit associationFilename sys argv 1 xrefsFilename sys ar
78. at http java freehep org This product includes software developed by the Apache Software Foundation http www apache org This product includes software developed by the JDOM Project http www jdom org One step installation of the Cytoscape software is accomplished using the InstallAnywhere product from ZeroG Software Inc http zerog com Appendix A Old Annotation Server Format Handlers for the following format still exist in Cytoscape as legacy code however we strongly recommend using the new formats OBO Gene Association described in the previous section since they are easier to download directly from the Gene Ontology project and use directly Currently users have no access to an import interface for this old format Building your own annotation files The annotation server requires that the gene annotations and associated ontology of controlled vocabulary terms follow a simple format This simple format was chosen because it is efficient to parse and easy to use The flat file formats are explained below The Ontology Format By example the Gene Ontology GO curator GO type all 0003673 Gene Ontology 0003674 molecular function partof 0003673 0008435 anticoagulant isa 0003674 0016172 antifreeze isa 0003674 0016173 ice nucleation inhibitor isa 0016172 0016209 antioxidant isa 0003674 0045174 glutathione dehydrogenase ascorbate isa 0009491 0015038 0016209 0016
79. ault Label Spring Length The desired length between the label and the node that the label belongs to Users can also choose to move the network nodes This option can be activated by enabling the Allow nodes to move option All network nodes or just the selected ones will be moved according to the Force Directed layout algorithm while making use of the Default Spring Coefficient Default Spring Length and Default Percentage 96 fields Default Spring Coefficient The strength of the pull between a network node and its connected neighbours The larger the value the closer the distance between the two objects will be to the Default Spring Length value Default Spring Length The desired length of an edge that is connecting two network nodes together Default Percentage The percentage of the total Number of Iterations in which you would like the algorithm to move the network nodes as well in addition to strictly moving the labels For example Number of Iterations 200 Default Percentage 96 80 Then the network nodes will be moved for 80 100 200 160 of the 200 iterations Other algorithm settings include Default Node Mass The mass that a default network node should take on Nodes with a greater node mass require more strength to move Number of Iterations The total number of times to run the algorithm for each execution of this label layout Reset the label position of all nodes Reposition the labe
80. been assigned to The rules are rather lax though for example anything can be interpreted as a string and all numeric values will be accepted for a boolean or logical attribute where non zero will be interpreted as true and zero as false For integer attributes floating point values will be converted using the rules of the Excel INT function Parentheses can be used for grouping and to change evaluation order The operator precedence rules follow those of standard arithmetic Operators Currently supported operators are the four basic arithmetic operators and the exponentiation operator and l are left associative and is right associative The string concatenation operator is amp Supported boolean or logical operators are the comparison operators lt gt lt gt and lt gt not equal Supported Functions Currently we support the following functions Cytoscape specific functions Degree the degree of a node nDegree the indegree of a node OutDegree the outdegree of a node e SourcelD the ID of the source node of an edge TargetID the ID of the target of an edge Numeric Functions Abs Returns the absolute value of a number ACos Returns the arccosine of a number ASin Returns the arcsine of a number ATan2 Returns the arctangent of two numbers x and y 48 Cytoscape User Manual e Average Returns the average of a group of numbers Cos Ret
81. bution 178 Cytoscape User Manual d If distribution of the work is made by offering access to copy from a designated place offer equivalent access to copy the above specified materials from the same place e Verify that the user has already received a copy of these materials or that you have already sent this user a COpy For an executable the required form of the work that uses the Library must include any data and utility programs needed for reproducing the executable from it However as a special exception the materials to be distributed need not include anything that is normally distributed in either source or binary form with the major components compiler kernel and so on of the operating system on which the executable runs unless that component itself accompanies the executable It may happen that this requirement contradicts the license restrictions of other proprietary libraries that do not normally accompany the operating system Such a contradiction means you cannot use both them and the Library together in an executable that you distribute 7 You may place library facilities that are a work based on the Library side by side in a single library to gether with other library facilities not covered by this License and distribute such a combined library provided that the separate distribution of the work based on the Library and of the other library facilities is otherwise permitted and provided that you do these two t
82. by defining filters and performing the Boolean operation between them Since Cytoscape 2 5 the filters are redesigned to provide more user friendly interfaces The newly designed filters preserve most of the functionality of the old filters while introducing more its API can also be used by other plugins The old filters are still preserved because there are still a few features are not implemented in new filters and many users already got used to the old ones Using New Filters By default you should see a filter icon 5d If you click on it the filters tab on the Control Panel will be selected You can also access the filters by clicking directly on the tab or by using the Select menu pull down and choose Use Filters menu item The filters panel initially looks like this on the toolbar E 2 Control Panel E X fg Network vizMapper Editor Filters urrent Filter ceo All 1 Filter Definition To create a new filter click the option button and select Create new filter from the list provided Enter a name for the new filter ES Create new Filter Ey Create new topology filter B Greate new Modelnteraction filter BI Create new Edgelnteraction filter i Delete Filter P Rename Filter 137 Cytoscape User Manual New Filter Name X New Filter name my First Filter Definition of simple filter When a new filter is created it is empty initially I
83. by a space etc 33 Examples Example 1 Cytoscape User Manual Example 1 E Example 1 networkl networkl A networkl B Example 1 PP B PP A PP B 34 Cytoscape User Manual Example 2 Example_2 M1 Example_2 M2 M1 A M2 B pp E Example_2 A pp B Example_2 M1 im M2 35 Cytoscape User Manual Example 3 Example_3 M1 im M2 Example_3 M3 im M1 Example_3 M2 im M3 Example_3 E pp M3 Example_3 M2 pp E M1 A M2 A pp B M3 B pp 36 Example 4 File Edit View Select amp QAR Welcome to Cytoscape 2 7 0 Example 4 roor M1 M1 Example 4 M3 M2 M3 M3 M3 Example 4 Example 4 Example 4 Example 4 M1 M3 Cytoscape User Manual Layout Plugins Right click drag PP PP PP PP PP PP PP PP PP PP Help 37 Q 0 g ser FB E to ZOOM Middle click drag to PAN Cytoscape User Manual Example 5 File Edit View Select Layout Plugins Help Welcome to Cytoscape 2 7 0 Right click drag to ZOOM Middle click drag to PAN Example 5 M4 M4 D M4 M3 M3 M2 pp E M2 M1 pp B M1 A M4 E PP D GML Format In contrast to SIF GML is a rich graph format language supported by many other network visualization packages The GML file format specification is available at http www infosun fmi uni passau de Graphlet GML It is generally not necessary to modify the content of a G
84. cape User Manual Tutorial 2 Creating a New Visual Style with a Discrete Mapper The following tutorial demonstrates how to create a new visual style using a discrete mapper The goal is to draw protein DNA interactions as dashed blue lines and protein protein interactions as solid red lines Step 1 Load a sample network From the main menu select File gt Import gt Network Multiple file types and select sampleData galFiltered sif Step 2 Open the VizMapper Select the View Open VizMapper menu option or select the VizMapper icon in the main button bar or click on the VizMapper tab in the Control Panel at the left of the screen Step 3 Create a new visual style Click the Options button and select Create new visual style Name your new style Tutorial VS2 Step 4 Choose a visual attribute Double click the Edge Color entry listed in Unused Properties Edge Color will now appear at the top of the list under the Edge Visual Mapping category as shown below visual Mapping Browser Edge Color Please select an attribute Mapping Type Y Unused Properties Frine Ennt Fare Mnuhle Plirk tr rreate Step 5 Choose a network attribute Click on the cell to the right of the Edge Color entry and select in teraction from the dropdown list that appears Step 6 Choose a mapping type Set the Discrete Mapper option as the Mapping Type All available at tribute values for interaction will be display
85. cape User Manual eS a LP TM ITI EE TTE IE TEE ga a rn a LITT i ike Bie ke ed ee Die Peer Te er EA er m Str EE AN ES A oan A LLL mn El pien u els e o A Ve AAA RE LLL De heres ger pr Ai ua B Lus CEEE LIT ELI LEFID tm aaa ns IF i Gehi viner ee DII EI a rn E HFH ee Ka IT NT HILL H J A Hit er PU O n ee ed eg ee ae DL LL BLEPFLIL i le IEF a X ILLINS er LETEL PR ES db 401222 BLE Til Fi LIAE Li ek PEN Owen del pales Le De ILI L PI LELGLIL LI A pode ra an a ag PII UL Zeie igh De NER pre eq eld eg r Apra ee ee dra Pee pe T II EE T D c HIE ees und m nd el rd Al S EIL mp k m dl re dees reem ee MI NA ed epg Een bi ese epee FL pn ee l pram n e Visualize gene expression data along a color gradient 89 Cytoscape User Manual Control edge transparency opacity using edge weights 90 Cytoscape User Manual DN Py Ce er dos Dat De E E res reine aedem Pis Tibie Din ot Y en re M agerem tus Pepe bora me int T T d ruau aaae B H G 9 PI Ls E Browse extremely dense networks by controlling the opacity of nodes 91 Cytoscape User Manual e Show module locations in a large network Overlay a subnetwork on huge interactome using opacity and color control 92 Cytoscape User Manual Pagina RS s F Pizai pang 2 P Cytoscape 2 6 0 and later has additional sample Visual Styles You can try tho
86. characters can be inserted into String attributes either by pressing Enter or by typing n Once finished editing click outside of the editing cell in the Attribute Browser or press Shift Enter to save your edits Pressing Esc while editing will undo any changes Attribute rows in the browser can be sorted alphabetically by specific attribute by clicking on a column heading A new attribute can be created using the Create New Attribute O button and must be one of four types integer string real number floating point or boolean Attributes can be deleted using the Delete Attributes Kam D button NOTE Deleting attributes removes them from Cytoscape not just the attribute browser To remove attributes from the browser without deleting them simply unselect the attribute using the Select A t t r 1 b u t e S E button The right click menu on the Attribute Browser has several functions such as exporting attribute information to spreadsheet applications For example use the right click menu to Select All and then Copy the data and then paste it into a spreadsheet application Each attribute browser panel also has a button for importing n e W a t t r i b u t e S The Node Attribute Browser panel has additional buttons for loading Gene Expression attribute matrices as node attributes Attribute Batch Editor eoe Node Attribute Batch Editor ion Copy Clear canonicalName
87. cya Contra Panyi Z 1600 vta t Hose puality Af Setup Phani Cox 5 Network MigMapger KA T Current Visual ile e Cutter Becwier r a e 1 kafe ras Won 3 WW E a i iee PES Drfazts Mon L Lagen 116 Wk d toca she Bester 0 With Mage Brower epee bid L ug gem Ze Neste Nat Masc L Rank 3 1 is here WELT T ge Codes nt zeg Tet gt af cupra Vee kescht hee f KR DAS Soe 15 H 5a ijg 29 T ode Shape MODO Mode Samus A ELSA Tyre Donek Mason ask fi Dumani Eure koer 5 j Bester id ri Seed tet agen E Dci CH GA o Uranio Piri Modo bedir Cose mede Spe Ze BOs CoN Too Pare EC EI deso ES rass fem ri CO Bee To Set o OH CDRLS AR OA eeng Sea A n and enibe YREOTSC Ve deeg z Due LMU eg eating EA a A vid dione fue ude Lek er ee um m M YPROIST r ze tim wit prono oe Kai raga tee reglas ol gracing from H Nolo TF poene PROC A n YOL STW Compen re of De Medias poms morra mun trarderipbon tom meda compel 5 YLRA SOMWC Paute Pen herp Ker Eu messer EIA erie acrid ences GMA rara la E E ER Ke de PLZ TW CAMP depenia peche kw CK NS 8 Ear Spam gral radiation proteins PAMP Gapenden probro Koit 4 Clases VMAPOGW G ng tb A TED ace GALA cemal leiste Barren mete Ce Ce GRA copia SERE ALA Tog aoe ORIO E A BL olo TPH DEE Pe io H i YBRI1SEC Sober RO kDa of TIO and SCA compl PCl ipscfe erg
88. d can be seen and edited in the Attribute Browser The value of the attribute is a string representation of a property For example color is represented by 3 integers repres enting the RGB red green blue value of the color Different types of properties have different string representations When in doubt just use the right click menu to create valid attribute values Because bypass values are specified using normal attributes these attributes will persist between sessions only as long as you save your session If you don t save your session you will lose whatever bypass values you set Finding and Filtering Nodes and Edges QuickFind Cytoscape includes a Quick Find feature which enables you to quickly find nodes and edges 132 Cytoscape User Manual File Edit View Select Layout Plugins Help SE Lal a Q o default HH 3 Search for Configure matching nodes Quick Find edges Using Quick Find is very simple Here is how it works e Import a network For example load up sampleData galFiltered sif e Start typing in the text box For example enter yd The search box will automatically display a list of all matching nodes Search ydl013w ydl014w yalO23c ydlO30w ydl 63c e Select a matching node Cytoscape will automatically zoom in on the selected node Se default Search B 006 galFiltered sif 133 Cytoscape User Manual Configuring Quick Find Quick Find works by creating an
89. de its cys session file while the default properties will be applied at the beginning of subsequent sessions 23 Cytoscape User Manual Managing Bookmarks Cytoscape contains a pre defined list of bookmarks which point to sample network files located on the Cytoscape web server Users may add modify and delete bookmarks through the Bookmark manager accessed by going to Edit Preferences gt Bookmarks amp Bookmark manager network Ke Yeast Protein Protein Ideker T et al galFiltered Human Protein Protein HPRD Literature Curated In Human Protein Protein Rual et al Toward a protea Human Protein Protein Rual et al Subnetwork for Human Protein Protein Stelzl et al A human proteir Yeast Protein Protein Ptacek et al Global analysis c CAPO i There are currently two types of bookmarks network and annotation Network bookmarks are URLs pointing to network files available on the Internet These are nomal networks that can be loaded into Cytoscape The annotation bookmarks are URLs pointing to ontology annotation files The annotation bookmarks are only used when importing an ontology Managing Proxy Servers You can define and configure a proxy server for Cytoscape by going to Edit gt Preferences Proxies O Proxy Server Setting Use Proxy Proxy Settings Type Host name am y After the proxy server 1s set all network traffic related to loading a network from URL will pass thro
90. des the Target nodes and an optional edge interaction type 26 Cytoscape User Manual Import Network end Edge Attributes from Table Import Network from Table Data Sources Input File file cellarfusers kono workspace cytoscape ftestData galFinered xls Interaction Definition Source Interaction Column 1 Show Text File Import Options Preview Excel Workbook Yeast Network Sheet 1 Interaction Type Target Interaction ep gt Column 2 O Columns in BLUE will be loaded as EDGE ATTRIBUTES Left Click Edit Column Ric ht Click ON OFF Column S Column 1 Column 2 Column 3 e Boolean At amp Text Attr 1 A Column YKROZ6C YGR2 18W YGLOS 7W YLR249W YLR249W YLR233C YMR146C YDR429C YPROBOW YGL122C YGLOS7W YFROBOW YBRI18W YGLOS 7W YDR429C YFLO17C YALOOSW hos E ER db i an dU ee REI The Import Network from Table function supports delimited text files and single sheet Microsoft Excel Supported Files YOR204W false true true true true true true true true Workbooks The following is a sample table file abcd 1 345 abcd12346 abcd12347 abcd12348 abcd12349 abcd12350 abcd12351 abcd12352 abcd12353 A RR TT d 1 2344543 1 2344543 1 2344543 1 2344543 1 2344543 1 2344543 1 2344543 1 2344543 1 2344543 Select File source target interaction boolean attribute string attribute
91. des whose canonicalName starts with YDLOO followed by any other two characters you would type YDLOO The denotes any single character while the represents zero or more characters Full regular expression searching is supported although is not covered here Once the filter is defined it will be assigned a default descriptive name 143 Cytoscape User Manual Numerical Filter Use Filters Manage Filters Numeric Attribute Filter Create new Filter Remove selected Filter Available Filters Select All Filter Filter Name Node null 0 0 Mode canonicalMame YL Mode canonicalMame YC canonicalMame a nul with a value For numeric attribute Select graph objects of type Node that is Apply selected Filter The Numerical Filter also allows you to filter nodes or edges and presents you with a list of available at tributes This filter matches all values in the network of your selected attribute that are greater than less than or equal to a number you type in the search box Node Topology Filter E Use Filters Manage Filters Node Topology Filter Create new filter Remove selected filter Available Filters Filter Name ModeTopology Select All Filter Mode canonicalName YL EET S Mode canonic
92. developers Less of an advantage over competing non free programs These disadvantages are the reason we use the ordinary General Public License for many libraries However the Lesser license provides advantages in certain special circumstances For example on rare occasions there may be a special need to encourage the widest possible use of a certain library so that it becomes a de facto standard To achieve this non free programs must be allowed to use the library A more frequent case is that a free library does the same job as widely used non free libraries In this case there is little to gain by limiting the free library to free software only so we use the Lesser General Public License In other cases permission to use a particular library in non free programs enables a greater number of people to use a large body of free software For example permission to use the GNU C Library in non free programs enables many more people to use the whole GNU operating system as well as its variant the GNU Linux operating system Although the Lesser General Public License is Less protective of the users freedom it does ensure that the user of a program that is linked with the Library has the freedom and the wherewithal to run that program using a modified version of the Library The precise terms and conditions for copying distribution and modification follow Pay close attention to the difference between a work based on the library and a work that uses t
93. dges 29 Cytoscape User Manual Modify Attribute Name Type Set Atnbute Name and Type Attribute Name and Type Attribute name for Column 5 entry Attribute Data Type iw String Integer Floating Point Boolean CH List List Delimiter is Attribute names and data types can be modified here Modify Attribute Name just enter a new attribute name and click OK Modify Attribute Data Type The following attribute data types are supported e String Boolean True False nteger Floating Point ist of one of String Boolean Integer Floating Point Cytoscape has a basic data type detection function that automatically suggests the attribute data type of a column according to its entries This can be overridden by selecting the appropriate data type from the radio buttons provided For lists a global delimiter must be specified 1 e all cells in the table must use the same delimiter Import Networks from Web Services From version 2 6 0 Cytoscape has a new feature called Web Service Client Manager Users can access verious kinds of databases through this function Please read Importing Networks and Attributes from External Database for more detail Edit a New Network A new empty network can also be created and nodes and edges manually added To create an empty network go to File gt New gt Network gt Empty Network and then manually add network components using the Editor in CytoPanel
94. documents for this format is available at http www biopax org index html PSI MI Format The PSI MI format s a data exchange format for protein protein interactions It is an XML format used to describe PPI and associated data PSI MI XML format specification is available at http psidev sourceforge net mi xml doc user Delimited Text Table and Excel Workbook Cytoscape has native support for Microsoft Excel files xls and delimited text files The tables in these files can have network data and edge attributes Users can specify columns containg source nodes target nodes interaction types and edge attributes during file import Some of the other network analysis tools such as igraph http cneurocvs rmki kfki hu igraph has feature to export graph as simple text files Cytoscape can read these text files and build networks from them For more detail please read the Import Free Format Tables section section of the Creating Networks chapter 39 Node Cytoscape User Manual Network generated by igraph s Watts Strogatz small world model 50k nodes and 250k esges visu alized by Cytoscape You can import networks created by other applications using this Table Import feature Naming Issues in Cytoscape Typically genes are represented by nodes and interactions or other biological relationships are represented by edges between nodes For compactness a gene also represents its corresponding protein Nodes may also be
95. e Layout gt Scale option will open the Scale window in CytoPanel 5 This function will scale the position of the entire network or of the selected portion of the network Note that only the position of the nodes will be scaled not the node sizes Node size can be adjusted using the VizMapper The image below shows selected nodes scaled Before 78 Cytoscape User Manual eA eA CytoPanel 5 1 8 1 4 1 2 1 2 4 8 Y 5cale Selected Nodes Only After AAA sample ODO CytoPanel 5 Scale 1 8 1 4 1 2 1 2 4 8 M Scale Selected Nodes Only Align ela lalt ae LL a Distribute bb an 143 PSUS Stack amp lalsirfleliel Selecting the Layout gt Align Distribute option will open the Align Distribute Stack window in CytoPanel 5 The Align buttons provide different options for either vertically or horizontally aligning selected nodes against a line The differences are in what part of the node gets aligned e g the center of the node the top of the node the left side of the node The Distribute buttons evenly distribute selected nodes between the two most distant nodes along either the vertical or horizontal axis The differences are again a function what part of the node is used as a reference point for the distribution And the Stack buttons vertically or horizontally stack selected nodes with the full complement of alignment options The table below provides a decription of what each button does Descri
96. e URL is valid and an actual image data exists there Cytoscape automatically download the image and map it to the node Examples 1 Color Passthrough Mapping 103 Cytoscape User Manual Node Visual Mapping Mode Color Color as Text Mapping Type Passthrough Mapping YIJIROG6W silver YKLO 4C FFLA400 YKLO12W lime YLR116W red YORO46W green YNL236W pink 2 Node Size Passthrough Mapping 104 Cytoscape User Manual IL Node size as integers YLR116W 30 YNL236W 4 YGORO46W 50 YKLO12W 60 YJRO66W 150 YKLO74C 100 3 Custom Graphics Passthrough Mapping 105 Cytoscape User Manual Node Visual Mapping Node Custom Graphics 1 Graphics Location URL as Strings Mapping Type Passthrough Mapping ELUF 4 http www cytoscape org Images ago ju YKLO 1 2W Til H bie YORDA GH Bil XM TLE FOT 106 Cytoscape User Manual YGROAGW i YKLOL2W YLR116W UCSD m m YKLO74C YNL236W Y ROGOW Custom Graphics Manager Mame hip aww rcsb org pdhb images 3gz9 asr 250 iparbioNums 1 Tags bitmap image protein 3D POR Actual Size Wie Ripe Cond dies hod gdb Width 250 Height 250 Mi Aspect Ratio Original From Cytoscape 2 8 0 Cytoscape supports Custom Graphics for nodes You can add all kinds of bitmap images such as jpg png or gif on the top of network nodes From user point of view this is simply an addition to the Visual Properties and
97. e a while since it is a large data file Step 4 When Cytoscape finishes importing files the import window will be automatically closed All attributes mapped by this function have the prefix annotation and look like this annotation attrib ute name All ontologies will be added to the end of the Ontology DAGs branch in the Network Manager oco ogo 219740 34892 Generic GO slim 149 5 37 37 530 8480 0 8862 1 Ontology DAGs have some attributes associated with the terms All attributes associated with ontology terms will have the prefix ontology They have at least one attribute ontology name For more detailed information about attributes for ontology DAGs please read the official OBO specification document e Note Cytoscape supports both OBO formats version 1 0 and 1 2 Note Switching Primary Key for Go Annotation Import If node IDs in a network file are NOT DB_Object_Symbol 3rd column in Gene Association file you need to select a primary key column Click Show Mapping Options to change the key Usually DB_Object_ID can be an alternative primary key Custom Annotation Files for Ontologies Other than GO for Advanced Users The Import Ontology and Annotation function is designed to import general ontology and annotation files Internally mapping ontology terms onto existing networks is the same as joining three data tables 162 Cytoscape User Manual in Cytoscape An Ontology DAG an
98. e based on the CytoPanel state If the CytoPanel 1s docked clicking on the icon will float the CytoPanel as indicated by the Float Window tooltip Alternatively 1f the CytoPanel is floating clicking on the icon will dock the CytoPanel as indicated by the Dock Window tooltip jd r4 Float Dock Wincow Window Rendering Engine What is Level of Detail LOD In Cytoscape 2 3 a new network rendering engine is being introduced The goal of the rendering engine is to be able to display large networks gt 10 000 nodes yet retain interactive speed To accomplish this goal a technique involving level of detail LOD is being used Based on the number of objects nodes and edges being rendered an appropriate level of detail is chosen For example by default node labels if present are only rendered when less than 100 nodes are visible because drawing text is a relatively expensive operation This can create some unusual behavior If the screen currently contains 98 nodes node labels will be displayed If you pan across the network such that now 101 nodes are displayed the node labels will disappear As another example if the sum of rendered edges and rendered nodes is greater than or equal to a default value of 2000 a very coarse level of detail is chosen where edges are always straight lines nodes are always rectangles and no antialiasing is done The default values used to determine these thresholds can be changed by setting pr
99. e menu option and save the properties as a file This feature can be used to share visual styles with other users Importing Visual Styles To import existing visual styles navigate to the File gt Import gt Vizmap Property File menu option and selectavizmap props file Imported properties will supplement existing properties or override existing properties if the properties have the same name You can also specify a visual properties file using the V command line option cytoscape sh V myVizmap props Visual properties loaded from the command line will override any default properties Default Visual Styles It is possible to change the default visual properties for all sessions of Cytoscape To do this navigate to the Edit Preferences Properties menu option check the Make Current Visual Styles Default box in the Default Visual Styles section and click the OK button This will save the current visual styles as a vizmap props file to your cytoscape directory found in your home directory These visual styles will then be loaded each time Cytoscape is started Bypassing Visual Styles Cytoscape has a feature that allows users to override visualizations created by the VizMapper for individual nodes and edges This feature is available by right clicking on a node or edge and then clicking on the Visual Mapping Bypass menu 131 Cytoscape User Manual YGLO35C Change Node Visualization LinkOut Reset Node Col
100. e nodes each set of nodes that share the same value for the attribute are laid out in a separate circle The same network shown above subset of galFiltered is shown below using Layout Cytoscape Layouts Attribute Circle Layout Degree 73 Cytoscape User Manual Label Force Directed Layout The Label Force Directed Layout is an automatic label repositioning plugin that can be accessed through Layout gt Cytoscape Layouts gt Label Force Directed Layout The layout is designed to be applied to position labels after another network layout is run to position nodes It is compatible with any node po sitioning layout Specific numerical values that the algorithm makes use of can be set by the user through the Layout Settings menu Through adjusting these values you can control how much you want to spread the labels and or nodes of the network by This label layout can be applied to the entire network or only to those nodes that are selected through enabling the Only layout selected nodes option Upon the application of this plugin node labels will be repositioned according to the Force Directed algorithm using the Default Label Spring Coefficient and Default Label Spring Length fields Default Label Spring Coefficient The strength of the pull between the label of a node and the node itself The distance between nodes and their labels will be closer to the Default Label Spring Length if this value 1s larger Def
101. e nucleus amd separating irz coments Trom thee rast of the open incluidas ra merma CUERO nuclesplasm Tha part of The nuclear contem oiher an ihe cehremasames ar ihe nuclepius chm al alm diih h a D D a EI D D D d Pa ss D D 2m Hode Annbine Browser Edge Ar ribune Browser Metwork Attribute Brower 156 Cytoscape User Manual e Note 1 Some ontologies have a lot of terms For example the full Gene Ontology contains more than 20 000 terms If you need to save memory you can remove this ontology DAG from Network Panel right click on the ontology name at the left hand side of the screen and select Destroy Network e Note 2 All ontology DAGs will be saved in the session file To minimize the session file size you can delete the Ontology DAG before saving session Gene Association File The Gene Association GA file provides annotation only for the Gene Ontology It is a species specific annotation file for GO terms Gene Association files will only work with Gene Ontologies and NOT others Sample Gene Association File gene_association sgd annotation file for yeast SGD S0000023591I0 AADIO GO UDDOUSI SGD REF 5000042 Lol PMID LO SGD gt 0000052 73 AAD14 GO 0008372 SGD_ REF S0O00069584 ND Node Name Mapping If you have a network file and an attr bute file they should have a common key to map attributes onto network data If those two do not have a common key you need to do an extra step to add a shared key The
102. e options The Visual Mapping Browser at the bottom displays the mapping details for a given visual style and is used to edit these details as well 2 Default Appearance Editor 96 Cytoscape User Manual Default Appearance for default NODE_FILL_COLOR NODE_BORDER_COLOR NODE_SHAPE 40 0 NoDESIZE NODE_LABEL F O nt NODE FONT FACE NODE FONT SIZE Node Edge Global Dependencies e Clicking on the section labelled Defaults on the Main Panel will bring up this editor which allows users to visually edit the default appearance of nodes and edges for the selected visual style 3 Continuous Editors These are editors for continuous mapping which is a mapping from numerical value to visual attributes They are accessed through the Visual Mapping Browser on the Main Panel Using these windows users can edit continuous mapping more intuitively e Color Gradient Editor e Continuous to Discrete Editor e Continuous to Continuous Editor These editors will be discussed in further detail below Introduction to Visual Styles The Cytoscape distribution includes several predefined visual styles to get you started To demonstrate these styles try out the following example Step 1 Load some sample data Load a sample session file From the main menu select File Open and select the file sampleData galFiltered cys e The session file includes a network some annotations and sample visual sty
103. e palette onto the canvas To connect two nodes with an edge drag and drop an arrow shape onto a node on the canvas This node becomes the source node of the edge Move the cursor and a rubber banded line will follow the cursor As the cursor passes over another node that node is highlighted and the rubber banded line will snap to a connection point on that second node Click the mouse while over this node and the connection will be established 146 Cytoscape User Manual 1 a Cytoscape Version 25 File Edit View Select Layout Plugins Help 606 Cytoscape Desktop New Session E E i FT jaEGQQgaagags B Control Panel Ta eon Network D Network VizMapper Editor Filters Directed Edge Add a Node o O iw Welcome to Cytoscape 2 5 Right click drag to ZOOM Middle click drag to PAN You can abort the drawing of the edge by clicking on an empty spot on the palette Note that if you change the Visual Style the palette used by the current network view will also change to be consistent with the mappings in the new Visual Style There is also an Edit Connect Selected Nodes option that when chosen creates a clique amongst the selected nodes The editor provides accelerators for adding nodes and edges Control clicking at a position on the canvas creates a node at that position The NODE TYPE attribute of the node will be the same as the NODE TYPE of the node most recently added defaulting back to the original vis
104. e the slider to exact location 2 Min Max Button Set the overall range of this editor First time you open the editor the Min and Max values are set by the range of attribute you selected 1 e minimum and maximum value of the attribute will be set to the range of this editor You can change this range anytime you want by pressing this button 3 Add Handle Button Add a new handle to the editor 4 Delete Handle Button Delete selected handle from the slider widget Gradient Editor i e O e Gradient Editor for Node Color Continuous Mapping for Node Calor sl V V gt 1 0000 5 0000 10 0000 15 0000 Min 1 0 Degree Max 18 0 Range Setting io Min Max Add Delete 129 Cytoscape User Manual Gradient Editor is a editor to create continuous mapping for colors To change the color of each region just double click the handles small triangles on the top Color gradient will be created only when editor has two or more handles see the example below 1 Slider No Graient 2 Sliders Continuous Continuous Editor k 606 Continuous Editor for Node Size Continuous Mapping for Node Size Y Y v Node Size Min 1 0 1 0000 18 0000 15 0000 j Degree Max 18 0 of Add Delete E Continuous Continuous Editor is for creating mapping between numerical attributes and numeric
105. earch term in the URL link will result in a meaningful link Adding or Removing Links The default links are defined in a linkout props file contained in 1inkout jar These links are normal java properties and can be edited by going to Edit Preferences Properties New links can 166 Cytoscape User Manual be defined this way as well New links can be defined at startup in a separate file and loaded from the command line either by specifying a file containing the links cytoscape sh P new_linout props or as individual properties cytoscape sh P nodelinkouturl yeast SGD http db yeastgenome org cgi bin locus p Any links defined on the command line will supersede the default links To remove a link from the menu simply delete the property using Edit Preferences Properties Use LinkOut from Attribute Browser From Cytoscape 2 6 0 you can use LinkOut from Attribute Browser Basic functionality is the same and the only difference is the parameter passed to the LinkOut is value in the selected cell MENGT GERRIG DITA AA Fd ETA d acosa 115713 ENSGOO000 107643 MAPKS MARS NORA IFNSO00000197694 SPTANI KU Open as hyper link 00000182899 RPL35A KS Q15712 Copyall 00000180879 SSR 015713 Copy one entry 00000128245 Lite Lanas rr en E 3XX6 Gare EE eb Array Express a ENS EBI Tools CF ENSG IHOP Ha BTALA ENSG Entrez 16 u search Engines ENSG KEGG STD11 092779 D n Interaction Dat
106. easure expression values without a comparison The file consists of a header and a number of space or tab delimited fields one line per gene with the following format Identifier CommonName valuel value2 valueN pvall pval2 pvalN Brackets indicate fields that are optional The first field identifies which Cytoscape node the data refers to In the simplest case this is the gene name exactly as it appears on the network generated by Cytoscape case sensitive Alternatively this can be some node attribute that identifies the node uniquely such as a probeset identifier for commercial microar rays The next field is an optional common name It is not used by Cytoscape and is provided strictly for the user s convenience With this common name field the input format is the same as for commonly used ex pression data anaysis packages such as SAM http www w stat stanford edu tibs S AM The next set of columns represent expression values one per experiment These can be either absolute expression values or fold change ratios Each experiment is identified by its experiment name given in the first line Optionally significance measures such as P values may be provided These values generated by many microarray data analysis packages indicate where the level of gene expression or the fold change appears to be greater than random chance If you are using significance measures then your expression file should contain them
107. ective to a Node or replace the assigned network at a node if there was a prior existing one In order to remove a nested network please pass null to this method e public GraphPerspective getNestedNetwork If a Node has an associated nested network it will be returned by this method If no associated nested network exists null will be returned instead Plugins and the Plugin Manager The Plugin Manager The Plugin Manager first introduced in Cytoscape 2 5 allows users to quickly and conveniently add extra features to Cytoscape directly from within Cytoscape eliminating the need for manual searches through different webpages to install and update plugins 148 Cytoscape User Manual For plugin developer to enable automatic download of your plugin to Cytoscape users your plugin should be in compliance with Cytoscape 2 5 or later and the plugin jar zip files should be uploaded to the Cytoscape plugin web site at http cytoscape org plugins php Note If you do not have Internet access enabled you will not see the list of available plugins or be able to automatically update existing ones however you will still be able to view and delete previously installed plugins Get New Plugins To install new features go to the Plugin Manager at Plugins Manage Plugins On the left side of the window that pops up you will see plugin folders labeled Currently Installed and Available for Install Double clicking on these will show sub fold
108. ed as shown below Y Edge Visual Mapping Y Edge Color interaction Mapping Type Discrete Mapping pd pp 115 Cytoscape User Manual Step 7 Set the mapping relationship Click the empty cell next to pd protein DNA interactions On the right side of the cell and X buttons will appear Click on the button A popup window will appear select blue and the change will immediately appear on the network window pd LJ d Repeat step 7 for pp protein protein interactions but select red as the edge color Then repeat steps 4 through 7 for the Edge Line Style attribute You can select the correct line style dashed or solid from the dropdown list Y Edge Visual Mapping Y Edge Color interaction Mapping Type Discrete Mapping pd Po pp A Y Edge Line Style interaction Mapping Type Discrete Mapping pd a LONG DASH pp a gt OLID Now your network should show pd interactions as dashed blue lines and pp interactions as solid red lines A sample screenshot is provided below 116 Cytoscape User Manual aaa E L3 aan EQ Key D E hparch Comal Panel da een II TT Eier fines EN Current Vismal Style Tutorial VS2 E el 3 Detaults B sens BE Visual Mapping Browser Cytoscape Desktop Session galFiltered cys le m Y Edge Visual Mapping 0 T Edge Color interaction Mapaing Type Discrete Mapping pa pn D F Edge Line Style interact
109. ed such as the Agilent Literature Search or Merge Networks De pending on which plugins are loaded the plugins that you see may be different than what appear here Manage Plugins Update Plugins Merge networks MCODE gt i Note A list of available Cytoscape plugins with descriptions is available online at http cytoscape org plu gins2 php The Help menu allows you to launch the online help viewer and browse the table of contents for this manual The About option displays information about the running version of Cytoscape 17 Cytoscape User Manual Contents Fl Contact Help Desk About Network Management Cytoscape 2 3 and newer versions allow multiple networks to be loaded at a time either with or without a view A network stores all the nodes and edges that are loaded by the user and a view displays them You can have many views of the same network Networks and their optionally associated views can be organized hierarchically An example where a number of networks have been loaded and arranged hierarchically is shown below 606 Cytoscape Desktop New Session eG QQgag egw JB Control Panel k VizMapper Editor H P hog vee c Nodes Edot 2254000 561562111 6710 34110 500 2700 300 3900 600 2500 2700 10110 CORE a W et Cluster 5 Welcome to Cytoscape 2 5 Right click drag to ZOOM Middle click drag to PAN The network manager top ri
110. eful tool for discovery of the list of built in functions Arguments can either be selected from a list of named attributes or constant values can be entered in a text entry field A major shortcoming at this time is that the Formula Builder won t let you compose functions with function calls as arguments If you need the most general functionality please type the expression directly into a cell 51 Cytoscape User Manual A Note for Plugin Writers It is relatively easy to add your own built in formula functions A simple function can probably be imple mented in 15 to 20 minutes It can then be registered via the parser and becomes immediately available to the user It will of course also show up in the drop down list in the formula builder Loading Gene Expression Attribute Matrix Data In addition to normal node and edge attribute data Cytoscape also supports importing gene expression data Gene expression data are imported using a different file format than normal attributes however the resulting attributes are not treated differently by Cytoscape Gene expression data like attribute data can be loaded at any time but are generally only relevant once a network has been loaded Data File Format Gene expression ratios or values are specified over one or more experiments using a text file Ratios result from a comparison of two expression measurements experiment vs control Some expression platforms such as Affymetrix directly m
111. el CytoPanel 1 the attribute browser CytoPanel 2 the Network Overview in CytoPanel 1 and the VizMapper MEA Select Layout Plugins Help Hide Control Panel i Hide Data Panel f Show Results Panel N Show Tool Panel Hide Graphics Details Qucm Si Open VizMapper S Open Custom Graphics Manager Arrange Network Windows p Select The Select menu contains different options for selecting nodes and edges It also contains the Select Use Filters option which allows filters to be created for automatic selection of portions of a network whose node or edge attributes meet a filtering criterion 16 Layout Cytoscape User Manual em Layout Plugins Help Mouse Drag Selects b Nodes Edges p Select all nodes and edges MA Deselect All Nodes and Edges VGA Use Old Filters Use Filters F7 The Layout menu has an array of features for visually organizing the network The features in the top portion of the network Rotate Scale Align and Distribute are tools for manipulating the network visual ization The bottom section of the menu lists a variety of layout algorithms which automatically lay a network out Layout Plugins Help Rotate Scale Align and Distribute Settings J yFiles je JGraph Layouts p Cytoscape Layouts Plugins Help The Plugins menu contains options for managing install update delete your plugins and may have options added by plugins that have been install
112. elected Edges turns a curved edge back into line segments View ESE Layout Plugins Help Mouse Drag Selects Leg Q Hodes 3 H4 py Search CET inver selection v1 Hide selection XH Select all nodes and edges ANA Show All 4H Deselect All Nodes and Edges V A Select all edges A se Filters F7 Deselect all edges XA Smooth selected edges Straighten selected edges Node Movement and Placement In addition to the ability to click on a node and drag it to a new position Cytoscape now has the ability to move nodes using the arrow keys on the keyboard By selecting one or more nodes using the mouse and clicking one of the arrow keys gt T J the selected nodes will move one pixel in the chosen direction If an arrow key is pressed while holding the Shift key down the selected nodes will 10 pixels in the chosen direction Mouse movement has also been enhanced If the Shift key is held down while dragging a node the node will only move horizontally vertically or along a 45 degree diagonal Visual Styles What Is a Visual Style One of Cytoscape s strengths in network visualization is the ability to allow users to encode any attribute of their data name type degree weight expression data etc as a visual property such as color size transparency or font type A set of these encoded or mapped attributes is called a Visual Style and can be created or edited using the Cytoscape VizMapper With the VizMapper the vi
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114. ers and then the plugins themselves To find out more about a specific plugin click on its name to display some basic information on the right hand side of the window ry ry Manage Pig Plugins avasable for download from Cyroscame A Curang installed 14 y oralik Erlrase la r mal SEM Reader 0 5 bp 1 0 L s rgo Lise 2 0 Deria Foie 0 5 A pupa ihat queres ther cPacs dacabase Sor precio Aoma iiai 1 0 ET ark SS rer ee ajhai Released By Tas rest 0 5 Fires 0 1 em Maut ess 1 0 CeopcapeEdior 2 0 Cid Patera ZO anche 1 0 Change Cownload Site Dele Close The Currently Installed folder contains a number of default plugins that are fully integrated in every copy of Cytoscape as well as any additional installed plugins In contrast the Available for Install folder displays plugins that may be installed To install and use these plugins click on the file name and then click on the Install button at the bottom of the window A license agreement may appear in which case you must accept it in order to download the plugin You will then see a progress bar as the plugin is automatically downloaded and installed into your current version of Cytoscape The progress bar will disappear when the download is complete Other plugins can then be downloaded or the manager can be closed by clicking the Close button Once a new plugin is added it can immediately be used Closing and restarting Cytoscape is not required For exam
115. evious installation directory and the cytoscape directory 2 Just keep what you have and simply pick a distinct new directory for installation In the unlikely event that you should encounter any problem delete the props files in your cytoscape directory If that doesn t help try deleting the cytoscape directory This latter step will cause you to loose all your plugins that you have installed via the plugin manager so only do that if you are having problems or if you don t mind reinstalling your plugins The core plugins will not be affected by this step There are a number of options for downloading and installing Cytoscape All options can be downloaded from the http cytoscape org website Automatic installation packages exist for Windows Mac OS X and Linux platforms Cytoscape User Manual You can install Cytoscape from a compressed archive distribution You can build Cytoscape from the source code e You can check out the latest and greatest software from our Subversion repository Cytoscape installations regardless of platform containing the following files and directories Licence files for the various libraries distributed with Cytoscape Directory containing cytoscape plugins in jar format ewo OO oooO galFiltered cys Sample session file created from datasets above plus annotations from several databases BINDyeast sif Network of all yeast protein protein interactions in the BIND database as of Dec 2006
116. functions by right clicking anywhere on the Visual Mapping Browser shown below Minen ales t Delete mapping o Generate Discrete Values d Rainbow 1 Modify Discrete Values k Rainbow 2 w modulations T Edit selected values at once Randomize Y Lock Node Width Height series Number Only emm PH Fit Node Width to Label 4 75 0 Automatic Value Generators Generate Discrete Values Functions in this menu category are value generator for discrete mappings Users can set values for discrete mappings automatically by these functions 126 Cytoscape User Manual Rainbow 1 and Rainbow 2 These functions try to assign as different colors as possible to each values see the example below Y Node Color Degree Mapping Type Discrete Mapping 1 H 3 4 5 6 T 8 d 11 17 18 Randomize Randomize colors and numbers If you use this function for numerical values node size Opacity etc you need to specify a range For example if you want to set values from 1 to 100 you need to type 00 in the dialog e Series Set series of numbers to the specified mapping D o Visual Mapping Browser DK Y Node Size Degree Mapping Type Discrete Mapping 0 0 35 0 50 0 65 0 30 0 95 0 110 0 125 0 140 0 155 0 ub Ee 3 n ap bh ww Kh ra Eech uoc 127 Cytoscape User Manual e Fit node size to label This function is only for node width and height When node size is
117. g from data attributes to visual attributes colors shapes and so on The section on visual styles discusses this in greater detail Cytoscape Attribute File Format Node and edge attribute files are simply formatted a node attribute file begins with the name of the attribute on the first line note that it cannot contain spaces Each following line contains the name of the node followed by an equals sign and the value of that attribute Numbers and text strings are the most common attribute types All values for a given attribute must have the same type For example FunctionalCategory YALOOIC metabolism YAROO2W apoptosis YBLOO7C ribosome An edge attribute file has much the same structure except that the name of the edge is the source node name followed by the interaction type in parentheses followed by the target node name Directionality 41 Cytoscape User Manual counts so switching the source and target will refer to a different or perhaps non existent edge The fol lowing is an example edge attributes file InteractionStrength YALOO1C pp YBRO43W 0 82 YMRO22W pd YDL112C 0 441 YDL112C pd YMRO22W 0 9013 Since Cytoscape treats edge attributes as directional the second and third edge attribute values refer to two different edges source and target are reversed though the nodes involved are the same Each attribute is stored in a separate file Node and edge attribute files use the same format Node attrib
118. ght tree view in CytoPanel 1 shows the networks that are loaded Clicking on a network here will make that view active in the main window if the view exists green highlighted networks only Each network has a name and size number of nodes and edges which are shown in the network manager If a network is loaded from a file the network name is the name of the file Some networks are very large thousands of nodes and edges and can take a long time to display For this reason a network in Cytoscape may not contain a view Networks that have a view are highlighted in green and networks that don t have a view are highlighted in red You can create or destroy a view for a network by right clicking the network name in the network manager or by choosing the appropriate option in the Edit menu You can also destroy previously loaded networks this way In the picture above seven networks are loaded six green ones with views and one red one without a view 18 Cytoscape User Manual Certain operations in Cytoscape will create new networks If a new network is created from an old network for example by selecting a set of nodes in one network and copying these nodes to a new network via the File gt New Network option it will be shown as a child of the network that it was derived from In this way the relationships between networks that are loaded in Cytoscape can be seen at a glance Networks in the top part of the tree in the figure ab
119. gv 2 species Homo sapiens 1piToNPHash readGoaXrefFile xrefsFilename tester IPIOO0099416 print hash size np np d np np len ipiToNPHash print test map np np s gt NP_054861 np np s np np tester ipiTo bLoproc open bioproc txt w moltfune open molfunc txt TWT cellcomp open cellcomp txt w bioproc write species np np s type Biological Process curator GO n n molfunc write species np np s type Molecular Function curator GO n n cellcomp write species np np s type Cellular Component curator GO n lines open associationFilename read split n sys stderr write found np np d lines n np np len lines for line in lines if line find 0 or len line lt 2 continue tokens laine split Nt goOntology tokens 8 golDraw tokens 4 golb dgorpDroaw splru ttp ipiName fixCanonicalName tokens 10 if len ipiName 1 continue if not ipiToNPHash has key ipiName continue refseqName ipiToNPHash ipiName printName refseqName printName ipiName 174 Cytoscape User Manual if ipiName tester print np np s np np s has go term np np s np np tester i goOntology C cellcomp write np np s np np s n np np printName goID elif goOntology P bioproc write np np s np np s n np np printName goID
120. he Interaction Networks tab The Interaction Networks tab enables you to filter interactions by data source and or interaction type For example you can choose to restrict your network to direct physical interactions from HPRD and MINT only 59 Cytoscape User Manual Step 3 Select Network s Pathways Interaction Netwe Matching Interactions 182 Filters Optional e Sy All Filters v Ww Filter by Data Source Cancer Cell Map 1 MHPRD 112 M intact 70 MINT 126 INCI Nature Pathway Interaction Database 20 Reactome 3 Li SE Filter by Interaction Type Biochemical Reaction 2 IComplex 17 Complex Assembly 4 VI Physical Interaction 309 Retrieve Interactions Pathway Commons Options You can configure access options from the Options tab There are two retrieval options e Simplified Binary Model Retrieve a simplified binary network as inferred from the original BioPAX representation In this representation nodes within a network refer to physical entities only and edges refer to inferred interactions Full Model Retrieve the full model as stored in the original BioPAX representation In this representation nodes within a network can refer to physical entities and interactions By default the simplified binary model is selected 60 Cytoscape User Manual Future Directions As additional web service clients become available they will be made available via the Cyto
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123. hm Most of the Cytoscape layouts also partition the graph before performing the layout In addition many of these layouts include the option to take either node or edge attributes into account Some of these layouts are 69 Cytoscape User Manual Grid Layout The grid layout is a simple layout the arranges all of the nodes in a square grid This is the default layout and is always available as part of the Cytoscape core It is available by selecting Layout Cytoscape Layouts Grid Layout A sample screen shot is shown below Force Directed Layout The force directed layout is a layout based on the force directed paradigm This layout is based on the algorithm implemented as part of the excellent prefuse toolkit provided by Jeff Heer The algorithm is very fast and with the right parameters can provide a very pleasing layout The Force Directed Layout will also accept a numeric edge attribute to use as a weight for the length of the spring although this will often require more use of the Settings dialog to achieve the best layout This algorithm is available by selecting Layout gt Cytoscape Layouts gt Force Directed Layout gt unweighted or the edge attribute you want to use as a weight A sample screen shot showing a portion of the galFiltered network provided in sample data is provided below 70 Cytoscape User Manual A 00 galFiltered sif child Spring Embedded Layout The spring embedded layout is based on a
124. hon parseGoTermsToFlatFile py go YYYYMM termdb xml goOntology txt see below for Python script listing Obtain the association file for your organism GO maintains a list of association files for many organisms these files associate genes with GO terms The next step is to get the file for the organism s you are interested in and parse it into the form Cytoscape needs A list of files may be seen at http www geneontology org GO current annotations shtml The rightmost column contains links to tab delimited files of gene associations by species Choose the species you are interested in and click Download 170 Cytoscape User Manual Let s use GO Annotations EBI Human as an example After you have downloaded and saved the file look at the first few lines oP TR O00115 DRN2 HUMAN GO 0003677 PUBMED 9714827 TAS Se TR O00115 DRN2 HUMAN GO 0004519 GOA spkw IEA SE ER 000115 DRN2 HUMAN GO 0004531 PUBMED 9714827 TAS Note that line wrapping has occurred here so each line of the actual file is wrapped to two lines The goal is to create from these lines the following lines species Homo sapiens type Molecular Function curator GO 1P100010348 0003677 IPIO0010348 0004519 IPIO0010348 0004531 Or species Homo sapiens type Biological Process curator G0 NP 0015366 0006259 NP 001566 0006915 NP 005289 0007186 NP 647593 0006899 The first sample contains molecular function annotations for proteins and each p
125. ialog shows a default setting of Data Source Type Local meaning that network files from the local computer will be available for importing Choose the correct file by clicking on the Select button only file types that Cytoscape recognizes will be shown and then load the network by clicking on the Import button Some sample network files of different types have been included in the sampleData folder in Cytoscape Network files in SIF GML and XGMML formats may also be loaded directly from the command line using the N option eou Import Network Import Network File Data Source Type Zei Local Remote URL Please select a network file Select Import Cancel Load Networks from a Remote Computer URL import The Import Networks dialog is also capable of importing network files using a URL To do this set the Data Source Type to Remote and insert the appropriate URL either manually or using URL bookmarks Bookmarked URLs can be accessed by clicking on the arrow to the right of the text field see the Bookmark Manager in Preferences for more details on bookmarks Also you can drag and drop links from web browser to the URL text box Once a URL has been specified click on the Import button to load the network 25 Cytoscape User Manual 608 Import Network Import Network File Data Source Type C Local Remote URL d as Import Cancel fou can specify URL by the following eee OO e Ty
126. ies to it and any later version you have the option of following the terms and conditions either of that version or of any later version published by the Free Software Foundation If the Library does not specify a license version number you may choose any version ever published by the Free Software Foundation 14 If you wish to incorporate parts of the Library into other free programs whose distribution conditions are incompatible with these write to the author to ask for permission For software which is copyrighted by the Free Software Foundation write to the Free Software Foundation we sometimes make exceptions for this Our decision will be guided by the two goals of preserving the free status of all derivatives of our free software and of promoting the sharing and reuse of software generally NO WARRANTY 15 BECAUSE THE LIBRARY IS LICENSED FREE OF CHARGE THERE IS NO WARRANTY FOR THE LIBRARY TO THE EXTENT PERMITTED BY APPLICABLE LAW EXCEPT WHEN OTHER WISE STATED IN WRITING THE COPYRIGHT HOLDERS AND OR OTHER PARTIES PROVIDE THE LIBRARY AS IS WITHOUT WARRANTY OF ANY KIND EITHER EXPRESSED OR IMPLIED INCLUDING BUT NOT LIMITED TO THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE LIBRARY IS WITH YOU SHOULD THE LIBRARY PROVE DEFECTIVE YOU ASSUME THE COST OF ALL NECESSARY SERVICING REPAIR OR CORRECTION 16 INNO EVENT UNLESS REQUIRED BY APPLICABLE
127. ifying the filename using the m option at the command line If you use the command line input you must enter your expression data by node ID If you use the dialog box then you can either load expression data by node ID the default option or you can select a node attribute to use in assigning your expression data to your Cytoscape nodes If you do use a node attribute then 1 the at tribute should already be loaded and 2 the node attribute value must match the first column in your matrix file Worked Example For the sample network file sampleData galFiltered sif Option A Load a sample gene expression data set by going to File gt Import gt Attribute Expression Matrix In the resulting window in the field labeled Please select an attribute or expression matrix file use the Select button to enter sampleData galExpData pvals The identifiers used in this file are the same ones used in the network file sampleData galFiltered sif so you do not need to touch the field labeled Assign values to nodes using A few lines of this file are shown below GENE COMMON gallRG gal4RG gal80R gallRG gal4RG gal80R YHROSIW COXO 0 0352 Et E 0 302 3 75 20891 1 9562406902 7 915406 090 YHRIZAW NDTS0 0 090 0 007 0 348 2 7014606 01 9 645306 01 3 4476006 01 XIEHEOLW PERSOSI 1567 90 253 Q40L2 06 2171206905 7 994006 04 1 240606 07T Option B Step 1 After loading the network load the node attribute file sampleData gal probeset
128. in a second set of columns after the expression values The column names for the expression significance measures need to match those of the expression values exactly For example here is an excerpt from the file galExpData pvals in the Cytoscape sampleData directory GENE COMMON gal1RG gal4RG gal80R gallRG gal4RG gal80R YHBOOSAW COXO 00254 0 211 0 302 3 59720e0 01 1062 40e 0Z 191340806 YHR124W NDT80 0 090 0 007 0 348 2 71460e 01 9 64330e 01 3 44760e 01 YKULGIW PROl 0 L6F 20 2255 0 417 06 27120e605 7 99400e 04 t 44060e 01 YXGROT2W UPES 0 245 0 471 0 787 4 104506 04 7 517606 04 1 371306 095 This indicates that there is data for three experiments gall RG gal4RG and gal80R These names appear two times in the header line the first time gives the expression values and the second gives the significance 52 Cytoscape User Manual measures For instance the second line tells us that in Experiment gall RG the gene YHRO51W has an expression value of 0 034 with significance measure 3 75720e 01 Some variations on this basic format are recognized see the formal file format specification below for more information Expression data files commonly have the file extensions mrna or pvals and these file extensions are recognized by Cytoscape when browsing for data files General Procedure Load an expression attribute matrix file using File gt Import gt Attribute Expression Matrix to bring up the import window or by spec
129. in miste col gr AGA complex SRI CACA Hor YLLO22C Hana qme MA phe ar re Ph Retest e ITE IA Dr ET YLRIS2C Dualfywron ragen arme ls of ZU geg EMA S omene m iayo D sen insaten face CH a E iE le k all Mode Amributetrowser Edge Amnbute Browier Network Attnbute Browser Wolters ba Cytedeape 2 5 Right click drag to ZOOM k dihe Hk drag ba PAM The user can then choose to resize hide or float CytoPanels For example in the screenshot below the user has chosen to float all panels and toolbar i EE Cuhebcape Verran Lt F r L t Wes Seng lar Fagas Hip i F e e Dro Zeroat e Daskiog heise peat cy KL P OH e u f pO CD Limon Toc I T eri Pace MECH bau E ou Fang Thins Baa anms Toni t Sete Wiles ee k a uad ww Pat Aa Ft ipi D Mikii L at Biye kin Me Si bed s Caters e LKA ta Mapping ener d e W Ea oda Vaga Mag ry a Z T Nodes Colo WOEN score e Mg Tra Dotan Pee Gare Vana Fre Pyy CR Ce WA omocs SA I REA MCCC ada Juan Be Sun Aleph ali aai Bikers Typa Ba Wik Eiai O aW z la EI E LH 3 nine O wech That kriise ra C Dee A i m al A RED E T pam Poet Tikk Dua Pipa kote Herde Caine m E d E hi E d ed von Mohr aps SE D se a mare aon Ed cmt ka Banaran aor d lest A eee FEES ek SAAT xw hr ger L6 TE 8 Aa Api A i BDH A A panda Passed ia a AA ry TL Lee nee ru Frai eget Dee roi G
130. ing annotation sequence and interactions e Biomart an open source biological database engine Useful for ID Name mapping All of these clients are available as Plugins and users can install them through Plugin Manager In the following sections users learn how to import network from extrenal databases Getting Started To get started select File Import Network from web services View Select Layout Plugins Help te Se ytoscape Desktop New Session E Network multiple file types Network from web services Mode Attributes Edge Attributes Attribute Expression Matrix E Vizmap Property File Import Attributes from NCBI Entrez Gene Import attributes from Biornart Tip View the animation demo for importing networks from web services Example 1 Retrieving Protein Protein Interaction Net works from IntAct e Select File gt Import gt Network from web services From the pull down menu select the IntAct Web Service Client e Enter one or more search terms such as BRCA1 e Click the Search button 56 Cytoscape User Manual Import Network from Database Import Network From Database Data Source IntAct Web Service Client Query search Property After confirming the download of interaction data the network of BRCAI will be imported and visualized bed iac LSD Visual Mapping Bypass Use Web Services IntAct Web Service Client Ger neighbours by
131. ion Mapping Type Discrepe Mapping pd a LONG DASH pa a SOLID Y Umed Properties Edge Font Face Edge Font Size Edge Laba Edge Label Color H T Welcome to Cytoscape 2 5 Tutorial 3 Visualizing Expression Data on a Network The following tutorial demonstrates how to create a new visual style using a continuous mapper The goal is to superimpose gene expression data onto a network and display gene expression values along a color gradient Step 1 Load a sample network From the main menu select File Import Network Multiple file types and select sampleData galFiltered sif Step 2 Load sample expression data From the main menu select File gt Import gt Attribute Expression Matrix and select sampleData galExpData pvals Step 3 Open the VizMapper Select the View Open VizMapper menu option or select the VizMapper icon in the main button bar or click on the VizMapper tab in the Control Panel at the left of the screen Step 4 Create a new visual style Click the Options button and select Create new visual style Name your new style Tutorial VS3 Step 5 Choose a visual attribute Double click the Node Color entry listed in Unused Properties Node Color will now appear at the top of the list under the Node Visual Mapping category Step 6 Choose a network attribute Click on the cell to the right of the Node Color entry and select gall RGexp from the dropdown list that appears 117 Cytoscape U
132. is rule is the MacOS platform if you are launching Cytoscape by clicking on the Cytoscape icon In that case you will have to edit the Cytoscape app Contents Info plist file instead For example if you want to assign 1GB of memory create the Cytoscape vmoptions file containing the single line Do not forget the linefeed at the end of the line Xmx1GB Stack Size There is one more option related to memory allocation Some of the functions in Cytoscape use larger stack space a temporary memory for some operations such as Layout Since this value is set independently from the Xmx value above sometimes Layout algorithms fails due to the out of memory error To avoid this you can set larger heap size by using the Xss option If layout fails for large networks please try the following XmxIGB Xss10M The option Xss70M means set the heap size to LOMB In many cases this solves out of memory error for Layouts 11 Cytoscape User Manual Randomly generated scale free network with 500K nodes and 500k edges If memory parameters are set properly you can visualize huge networks In this example about 5GB of memory is used by Cytoscape Stack size is set to 10MB To use large memory space 4GB you need 64 bit version operating system AND 64 bit version Java SE 5 or 6 Note Some of the web service clients are multi thread programs and each thread uses the memory size specified by Xss option If web service clients fails due
133. is the value used for mapping between the annotation file and network Usually the node edge ID is used as the primary key but you may choose any of the available attributes The Ontology term ID is the key used for mapping between the annotation file and the ontology DAG Using these data sources you can annotate network objects in Cytoscape Suppose you have a small network node_l pp node_2 node_3 pp node_l node_2 pp node_3 and you want to annotate this network with Ontology A which is an ontology DAG available in OBO format In this case you need an annotation table file that looks like this node 1 OA 0000232 node 2 OA 0000441 node 3 OA 0000702 where OA represents an ontology term ID This example is a file with the minimum necessary number of columns however you can include additional columns that will appear as additional node attributes Some ontologies will be used to annotate edges or networks For example the Protein protein interaction ontology is a controlled set of terms for annotating interactions between proteins so ontology terms should be mapped onto edges see example below node 1 pp node 2 MI 0445 node 3 pp node 1 MI 0046 node 2 pp node 3 MI 0346 164 Cytoscape User Manual Import nrag Data and ATmotations Import Ontology and Annotation Amoles Hode mW Edge Meta rk Annotation 7 Local Annotation File edgeAssociation txt Ontology i Frotein protein interaction Adv
134. itutes of Health NIH under award number GM070743 01 Corporate funding is provided through a contract from Unilever PLC Introduction Cytoscape is a project dedicated to building open source network visualization and analysis software A software Core provides basic functionality to layout and query the network and to visually integrate the network with state data The Core is extensible through a plug in architecture allowing rapid development of additional computational analyses and features Cytoscape s roots are in Systems Biology where it is used for integrating biomolecular interaction networks with high throughput expression data and other molecular state information Although applicable to any system of molecular components and interactions Cytoscape is most powerful when used in conjunction with large databases of protein protein protein DNA and genetic interactions that are increasingly available for humans and model organisms Cytoscape allows the visual integration of the network with expression Cytoscape User Manual profiles phenotypes and other molecular state information and links the network to databases of functional annotations The central organizing metaphor of Cytoscape is a network graph with genes proteins and mo lecules represented as nodes and interactions represented as links i e edges between nodes Development Cytoscape is a collaborative project between the Institute for Systems Biology Leroy
135. l Style dropdown list found at the top of the VizMapper Main Panel For example if you select Samplel a new visual style will be applied to your network and you will see a white background and round blue nodes Additionally if you zoom in closer you can see that protein DNA interactions specified with the label pd are drawn with dashed red edges whereas protein protein interactions specified with the label pp are drawn with a solid light blue edge see sample screenshot below mo Ssgaaaa gog Ann vaso Dip Chae Same gad ed eil i qa Sep et 98 Cytoscape User Manual Finally if you select Solid you can see the graphics below BAF vas Dita gie Same gal ered ay eLnaamauuduiuig B DEE galea D ee o e o E o e e a e o S o o e o a 0 86 25 e Ba o e a e e nd ee a e e he D a o e e 9 e o e gt ee o e a z b ge o CR e o e e o This Visual Style does not have mappings except node edge labels but you can modify the network graphics by editing Default View Additional sample styles are available as sampleStyles props file in the SampleData directory You can import the sample file from File Import Vizmap Property File Visual Attributes Graph Attributes and Visual Mappers The Cytoscape VizMapper uses three core concepts A visual attribute is any visual setting that can be applied to your network For example you can change all nodes from circles to
136. l of each node to their default position Note In order to yield the best layout for the labels this plugin may need to be executed more than once Before 74 Cytoscape User Manual b s Ton Were Zeie Lem Plugins Help SH aana Y A gt Ch Memori Visual 75 Cytoscape User Manual Fie Ei Tire Delt laca Fugint Help BH 124084 Y Aa ie amp Tamra Fami C ineedit S SE fo BR Y Heron VirHapeer Finers Editor Cureem Visual Style mitochondrion Aaler d Soa bel d nucleus F A Defauhis r L a i cyfoplasm i nucleus d i Viaggi Mapping Arewrurr aul nucleus Medea Vou Ha Meade Labai annatation Go CEL cellular bud membrane Weeer Tax Faren Seen Integral to membrane Ra membrane AA plasma membrane Lous vn vacuolar membrane i Boge Fon Fara u intracellular e Layout Settings H ye mn ge cytoplasm membrane Lar eut Al garsthm integral to membra plasma membrane r bi ra Ca kee a Label orta Ciri Laycul kd n intracellular Ede Lares paky membrane Label Fesce Directed Lay Setriagas Edge Line Style plasma membrane Standard settings Eat Lise Widih Pamman graph before Du E Bang inar ni lun seemed nadas a a iow modes 10 reco Edge Source Age m p Algeritm zrpteg Edge source Amr Defaun Sonny Cosfliciem 5 064 Lage Source ANTA E zi e 1 Dau Searing Lad pit sno
137. lar locations in the network extracellular region mitochondrial intermembrane s 1 hit mitochondrial outer membrane 2 hits 15 hits Dynamic Filtering via Quick Find If you choose to index on a numerical attribute the Quick Find search box changes to a dynamic slider for quick filtering For example 1 Import a network such as sampleData galFiltered sif using File Import Network multiple file types 135 Cytoscape User Manual 2 Import an expression data file such as sampleData galExpData pvals using File gt Import gt Attribute Expression Matrix 3 Configure Quick Find to index the network using the gall RGExp attribute 9909 Configure Search Options for galFiltered sif Select Index Type ei Index Nodes Index Edges Select Attribute Search on Attribute gallRGexp Attribute Description No description available Sample Attribute Values 0 045 0 963 0 101 0 551 0 155 ES 4 Use the slider widget to automatically filter the entire network default HH Select ues Rz 1 102 035 Filters Filters allow you to quickly select multiple nodes or edges of interest by comparing node and edge attributes to properties you specify For example you can select all the nodes whose name contains a specific pattern 136 Cytoscape User Manual or whose numeric attribute value falls within a certain range You can also perform complex selection
138. ld be Ensembl Gene ID Attribute is the list of available attributes in current Cytoscape session and Data Type is the type of ID set of the attribute In this case Cytoscape uses JD as the key for mapping Because the sample network galFile tred sif uses Ensemble Gene ID for its node ID like YORO72W you need to select Ensembl Gene ID for Data Type So you need to know the type of ID set Entrez Gene ID UniProt Unified Acc Number Ensemble Gene ID etc of the attribute selected in the Attribute box Select attributes you want to import Note You cannot select too many attributes at once because BioMart server has maximum number of selectable annotations Press Import Now you can see the newly imported attributes on the Attribute Browser You may see some attribute names ends with TOP if there are multiple attribute values for a node This is an attribute taken from the first entry of the original list attribute r 606 Data Panel ID Ensembl Gene ID EntrezGene ID Sgd TOP PDB ID PFAM ID YER179W YER179W 856926 DMCI PF084 23 YER143W YER143W 856886 DDI1 211A PFODO77 PF00627 TER133W YER 133W 856870 GLC PF00 149 YER111C YER111cC 856847 KE PFO2292 PF00023 YER110C YER110C 856846 KAP123 PFO3810 PFO2985 YER103W YER 103W 856840 5544 PFODO 12 YELO39C YELO39C 856672 CYCY 1YEA 1YEB PF00034 YELO41W YELO 4 1W 856670 YEF1 PF01513 YHR174W YHR174W 856579 EN
139. les By default galFiltered Style is selected Gene expression values for each node will be colored along a color gradient between red and green where red represents a low expression ratio and green represents a high expression ratio using thresholds set for the gal4RGexp experiment bundled with Cytoscape in the sampleData galExp Data pvals file Also node size is mapped onto the degree number of edges connected to the node and you can see the hubs of the network as larger nodes See the sample screenshot below 97 ena Sab GG EX 8 ppg ane Cytoscape User Manual var Dtos gie haa gal red aya l a LTD oF STT T Ms m gt j hi Li am E 1 E mum LL l Fa A Ere A A E a d un E Fa u af i d i A Fi z hy E A p E Ki Ki 1 F X i ty D OON I F 5 j 7 K j d e y e NW D H hy d i E Ze m j EN am SS e i fs h dag a as a E geg sii LR gp oo p j va la B j zo CN m a n A iie amp Ms fe 5 da a L i 1 T e i l D ar j 1 r p ZA ly V9 a an a We 07 zd 1 1 p F o F Ki T Lum a LJ me s i en r a eme d P Fa ln A A ke rt e Eck d T u a Ba ri h Fi gt al d E a I r Fu j _ g EEN NS t i 9 Step 2 Switch between different Visual Styles You can change visual styles by making a selection from the Current Visua
140. load any available plugins and updates To change this setting open the Plugin Manager by going to Plugins Manage Plugins and click the Settings tab You may choose a site from a preset list of bookmarks Alternatively click the Add button to open the Add new Bookmark dialog and create a new bookmark After new book mark is created the Plugin Manager will refresh using that site Note Custom download sites added from the Plugin Manager are not currently saved when you exit Cytoscape CytoPanels What are CytoPanels CytoPanels are floatable dockable panels designed to cut down on the number of pop up windows within Cytoscape and to create a more unified user experience These panels used to be called CytoPanel 1 2 and 3 From 2 5 they are named based on their functions The following screenshot shows the file yeastHighQuality sif and GO annotations loaded into Cytoscape performed Force Directed layout enable Align and Distribute tools and then run MCODE plugin for the data sets In Control Panel at the left hand side of the screen the Network Manager Network Overview VizMapper Filters and Cytoscape Editor have been loaded On the bottom of the panel there is another CytoPanel called Tool Panel In the 150 Cytoscape User Manual Data Panel the Attribute Browser has been loaded In addition Result of the analysis by MCODE plugin is Shown in Result Panel at the right hand side aoe Evioscap Desktop apie gas
141. n interaction Delimiters Whitespace space or tab is used to delimit the names in the simple interaction file format However in some cases spaces are desired in a node name or edge type The standard is that if the file contains any tab characters then tabs are used to delimit the fields and spaces are considered part of the name If the file contains no tabs then any spaces are delimiters that separate names and names cannot contain spaces If your network unexpectedly contains no edges and node names that look like edge names it probably means your file contains a stray tab that s fooling the parser On the other hand if your network has nodes whose names are half of a full name then you probably meant to use tabs to separate node names with spaces 32 NNF Cytoscape User Manual Networks in simple interactions format are often stored in files with a si f extension and Cytoscape re cognizes this extension when browsing a directory for files of this type 2 7 note Cytoscape will use URL encode data in node edge attribute files to properly preserve non ASCII characters If this presents a problem there are two java system properties that can be used to turn off either or both of encoding or decoding Property cytoscape encode attributes can be set to false to turn off writing attribute files with URL encoding Property cytoscape decode attributes can be set to false to turn off decoding during reading Files u
142. ng on your preferred method of opening the application All of them will change Cytoscape s default memory parameters except starting from the command line Option A Command line startup All operating systems platforms Create a Cytoscape vmoptions file in the cytoscape directory Make sure to add exactly one JVM option per line and that the last line has a line break at the end The most popular and important option is Xmx followed immediately no spaces by the amount of heap memory You can add an M for megabytes or a G for gigabytes Other options you may use may depend on the particular JVM that you are running A typical Cytoscape vmoptions file would look like this Xmx5G Xss10M This file allocates a maximum of 5GiB of heap memory and 10MiB of stack space per thread Option B Using the Cytoscape icon Windows and or Linux systems Just like with Option A you can use the Cytoscape vmoptions file The problem with Windows is that the lines need to be terminated with a single line feed character a k a a newline character and must not contain any carriage return characters This is difficult to accomplish on Windows on which the default is line termination with carriage return line feed pairs You typically need to use a programmers editor and make sure to set the line end configuration to line feeds only Another option on Windows is to create the 181 Cytoscape User Manual Cytoscape vmoptions file on Mac OS or Li
143. nnotation to ease data in tegration This ontology is used to annotate protein names protein family names and generic concrete protein names in the INOH pathway data INOH is part of the BioPAX working group Event INOH pathway onto A structured controlled vocabulary of pathway centric biological processes logy This ontology is a INOH pathway annotation ontology one of a set of onto logies intended to be used in pathway data annotation to ease data integration This ontology is used to annotate biological processes pathways and sub pathways in the INOH pathway data INOH is part of the BioPAX working group Protein protein interaction A structured controlled vocabulary for the annotation of experiments concerned with protein protein interactions Pathway Ontology The Pathway Ontology is a controlled vocabulary for pathways that provides standard terms for the annotation of gene products PATO PATO is an ontology of phenotypic qualities intended for use in a number of applications primarily phenotype annotation For more information please visit the PATO wiki http www bioontology org wiki in dex php PATO Main_Page Mouse pathology The Mouse Pathology Ontology MPATH is an ontology for mutant mouse pathology This is Version 1 Human disease This ontology is a comprehensive hierarchical controlled vocabulary for human disease representation For more information please visit the Disease Ontology website http diseaseo
144. notice for the Library among them as well as a reference directing the user to the copy of this License Also you must do one of these things a Accompany the work with the complete corresponding machine readable source code for the Library including whatever changes were used in the work which must be distributed under Sections 1 and 2 above and if the work is an executable linked with the Library with the complete machine readable work that uses the Library as object code and or source code so that the user can modify the Library and then relink to produce a modified executable containing the modified Library It is understood that the user who changes the contents of definitions files in the Library will not necessarily be able to recompile the application to use the modified definitions b Use a suitable shared library mechanism for linking with the Library A suitable mechanism is one that 1 uses at run time a copy of the library already present on the user s computer system rather than copying library functions into the executable and 2 will operate properly with a modified version of the library if the user installs one as long as the modified version is interface compatible with the version that the work was made with c Accompany the work with a written offer valid for at least three years to give the same user the mater ials specified in Subsection 6a above for a charge no more than the cost of performing this distri
145. nshot 159 Cytoscape User Manual lo s Import Attribute from Table Dada founces Atuibutes Node Edge O Nerwork Input File f e cellar users kono workspace MameMappingFieP arser OriginalData human dic Cu ep Select File Advancnd a Shaw Mapping Optiens _ Sew Text File impor Optiens Annctation File io Aftribute Mapping Key Column in Annotation File Key Attribute for Network Primary Key dy EnarezGene Column tribute Name dp String EntrezGene HGNC Diiia Symbol Other Aliases Preview Text File Left Click Enable Disable Column Right Click Edit Column Legend BETTAN mamanak eyes key Attributes t UniProt s EntrezGene s HGNC s Official Symbol Other Aliases 100 Q9YNAS HERV K C19 Gaq HERV K 19912 provirus ancestral 2 10054 Q9Yv6r4 26236 20953 C orf354 Protein HGC6 1 Uncharacterized pr 1005977 SELTA 26238 21235 CGorfl 3 Protein C orfl 3 chromosome 6 10127 wh Q9Y6Y9 23643 17156 LY 96 MD 2 protem Lymphocyte antige 10174 CH QIYEYE 11196 170018 SEC23IF p125 P125 5EC23anteractinq pro A Q9Y6Y1 23261 18806 CAMTAL Calmodulin binding transcription 1020 Q9Y6x9 22880 23573 M R MORC family CWetype zine finger 10236 Q9Y6X8 22882 18513 ZHX2 KIAAO0854 Alpha fetoprotein requis 10248 1026 Key Matches 1 First 100 anes are loaded fer preview File Size 2972 Keyed lt listitem gt lt listitem gt Press Import The network has new n
146. ntology sourceforge net 155 Cytoscape User Manual Although Cytoscape can import all kinds of ontologies in OBO format annotation files are associated with specific ontologies Therefore you need to provide the correct ontology specific annotation file to annotate nodes edges networks in Cytoscape For example while you can annotate human network data using the GO Full ontology with human Gene Association files you cannot use a combination of the human Disease Ontology file and human Gene Association files because the Gene Association file is only compatible with GO Visualize and Browse Ontology DAG for Advanced Users Relationships between ontology terms are usually represented as Directed Acyclic Graphs DAGs This is a special case of a network or graph where nodes are ontology terms and edges are relationships between terms Originally Cytoscape used a special data structure called BioDataServer to store ontology DAGs Starting in version 2 4 ontology data will now be stored in the same data structure as normal net works This enables users and plugin writers to visualize browse and manipulate ontology DAGs just like other networks The following is an example of visualization of an ontology DAG Generic GO Slim Every ontology term and relationship can have attributes In the OBO files ontology terms have optional fields such as definition synonyms comments or cross references These fields will be imported as node
147. nux and then to copy it into the Windows installation directory N B this is not a problem on Linux If you have a 64 bit version of Windows and are running a 64 bit version of Java you can also try using this Cytoscape vmoptions file Option C Using the Cytoscape icon on Mac OS 1 In the Finder right click on the Cytoscape icon and select Show Package Contents 2 Go to the Contents folder and open the file info plist 3 In the Property List Editor expand the Root directory then Java and modify the VMOptions value as per Option A You may put multiple options separated by spaces here You probably have to right click the VMOptions entry and select Value type gt Array then click on the triangle in front of the VMOptions entry so that it points downward and on the icon at the end of the VMOptions to create a new item Add a single JVM option for each item e g Xms20M for Item 0 and Xmx2G for Item 1 4 Save and close the file 5 Open Cytoscape by double clicking on the icon 182
148. o remove a value from mappings de faults select Empty Custom Graphics Saving and Loading Custom Graphics In general saving and loading Custom Graphics is automatic When you quit from Cytoscape all of the Custom Graphics in the manager will be saved automatically There are two types of saving 1 To session file When you save current session to a file Custom Graphics used in Visual Styles will be saved to the file For example if you have a Visual Style with a discrete mapping for Custom Graphics 1 all Custom Graphics used in the style will be saved to the session file Other graphics will not be saved 110 Cytoscape User Manual in your session file This is because your image library can be huge when you add thousands of images to Custom Graphics Manager and it takes very long time to save and load the session file 2 Automatic saving to cytoscape images directory When you select File gt Quit all of Custom Graphics in the Manager will be saved automatically to your Cytoscape setting directory Usually it s YOUR HOME DIRECTORY cytoscape images In any case Custom Graphics will be saved automatically to your system or session and will be restored when you start Cytoscape or load a session Visual Styles Tutorials The following tutorials demonstrate some of the basic VizMapper features Each tutorial is independent of the others Tutorial 1 Create a Basic Visual Style and Set Default Values The goal of this tuto
149. onnecting a node to itself self edges are also allowed nodel xx nodel Every node and edge in Cytoscape has an identifying name most commonly used with the node and edge data attribute structures Node names must be unique as identically named nodes will be treated as identical nodes The name of each node will be the name in this file by default unless another string is mapped to display on the node using the visual mapper This is discussed in the section on visual styles The name of each edge will be formed from the name of the source and target nodes plus the interaction type for example sourceName edgeType targetName The tag relationship type can be any string Whole words or concatenated words may be used to define types of relationships e g geneFusion cogInference pullsDown activates degrades inactivates inhibits phosphorylates upRegulates etc Some common interaction types used in the Systems Biology community are as follows ID IS cap Ma a e eene de a ve Beer protein protein interaction Dl urne d ai uae a RA AE protein gt DNA e g transcription factor binding upstream of a regulating gene Some less common interaction types used are DE and mer quee d e M protein gt reaction Di antonio ee f ah Sal reaction gt compound EE fd tits Sel rp compound gt reaction le MM genetic lethal relationship DI 3 545 duit esac A e a protein metabolite interaction oM re tat Ge a metabolite protei
150. operties Passthrough Map N N Node Label Color N N e Other Node Border Type Node Shape Node Label od od d lor od e City Node Label Width d t ly Node Label Position Edge Visual Mappings Edge Properties Passthrough Map Discrete Mapper Continuous Mapper per S QA A LA Ss Q z La Ry Qu S av z si a Mixx OS gt lt Ps gt lt PS gt lt OS gt lt a j a od E gz e e E P P PS PST S xxx g z e Ki e A A 102 Cytoscape User Manual x x EELER I x I X ge Soc Aron Color X x Ege Targe Arrow Opacity I X SX Edge Suc Aro Opa I X X Edge LabelColor o Fage Label Opaciy Numeric Edge Line Width erms o X X wea I X X Edge Source Aroa Shape X 9 x Edge Font Fam PR 9 Text Passthrough Mapper New feature from 2 8 X X xXx X X xXx Xx Xx x x From Cytoscape 2 8 0 Passthrough Mapper can recognize some text representations of values This means if you have an integer attribute named Node Size Values you can directly map those values as the Node Size by setting Node Size Values as controlling attribute name for Node Size Passthrough mapping The following is the supported value types Color Standard color names supported by all browsers or RGB representation in hex e Numerical Values Automatically mapped to the specified Visual Property Custom Graphics URL String If th
151. operties under Edit Preferences Properties Low LOD vs High LOD Large Network with Low LOD Large Network with High LOD 152 Cytoscape User Manual With low LOD values all nodes are displayed as square and anti alias is turned off With high LOD values anti alias is turned on and nodes are displayed as actual shape user specified in the Visual Style Parameters for Controlling LOD NOTE The greater these thresholds become the slower performance will become If you work with small networks a few hundred nodes this shouldn t be a problem but for large networks it will produce noticeable slowing The various thresholds are described below render coarseDetail If the sum of rendered nodes and rendered edges equals to or exceeds this number Threshold a very coarse level of detail will be chosen and all other detail parameters will be ignored If the total number of nodes and edges is below this threshold anti alias will be turned on this value defaults to 2000 render nodeBorder If the number of rendered nodes equals to or exceeds this number node borders Threshold will not be rendered this value defaults to 200 render nodeLa If the number of rendered nodes equals to or exceeds this number node labels belThreshold will not be rendered this value defaults to 100 render edgeArrow If the number of rendered edges equals to or exceeds this number edge arrows Threshold will not be rendered this value defa
152. opies of free software and charge for this service 1f you wish that you receive source code or can get it if you want it that you can change the software and use pieces of it in new free programs and that you are informed that you can do these things To protect your rights we need to make restrictions that forbid distributors to deny you these rights or to ask you to surrender these rights These restrictions translate to certain responsibilities for you if you dis tribute copies of the library or if you modify it For example if you distribute copies of the library whether gratis or for a fee you must give the recipients all the rights that we gave you You must make sure that they too receive or can get the source code If you link other code with the library you must provide complete object files to the recipients so that they can relink them with the library after making changes to the library and recompiling it And you must show them these terms so they know their rights We protect your rights with a two step method 1 we copyright the library and 2 we offer you this license which gives you legal permission to copy distribute and or modify the library To protect each distributor we want to make it very clear that there is no warranty for the free library Also if the library is modified by someone else and passed on the recipients should know that what they have is not the original version so that the original author s
153. or F Node Border Color Le Node Shape Reset Node Shape Node Size I a Node Label A Node Font Face Node Font Size Node Label Color Node Tooltip Node Label Position Node Line Width Node Line Style Node Opacity Node Label Opacity Node Border Opacity Reset All Each visual property of the node or edge is displayed When a property is overridden a checkmark appears next to the property and a Reset lt Property Name gt menu option appears directly below it By clicking this Reset option the bypass will be removed and the attribute will be displayed as defined by the VizMapper At the bottom of the menu a Reset All option appears When clicked this will remove all by passes for the specified node or edge In the example above you can see the selected node size color and shape have been overridden This is apparent in the appearance of the node itself and by the check marks in the popup menu It is important to realize that the Visual Mapping Bypass only works for individual nodes and edges and not for all nodes or edges of a specific type Using the bypass function is not particularly resource intensive meaning you can use it as much as you like However if you ever find yourself repeating the same bypasses then you should consider using the VizMapper instead Bypass is accomplished using special attributes with names like node fil1lColor and node shape These are normal Cytoscape attributes an
154. or executable form under the terms of Sections and 2 above provided that you accompany it with the 177 Cytoscape User Manual complete corresponding machine readable source code which must be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange If distribution of object code is made by offering access to copy from a designated place then offering equivalent access to copy the source code from the same place satisfies the requirement to distribute the source code even though third parties are not compelled to copy the source along with the object code 5 A program that contains no derivative of any portion of the Library but is designed to work with the Library by being compiled or linked with it is called a work that uses the Library Such a work in isol ation is not a derivative work of the Library and therefore falls outside the scope of this License However linking a work that uses the Library with the Library creates an executable that is a derivative of the Library because it contains portions of the Library rather than a work that uses the library The executable is therefore covered by this License Section 6 states terms for distribution of such executables When a work that uses the Library uses material from a header file that is part of the Library the object code for the work may be a derivative work of the Library even though the source code is not Wheth
155. ormat By example from the GO biological process annotation file species Saccharomyces cerevisiae type Biological Process curator G0 YMRO56C 0006854 YBRO85W 0006854 YJR155W 0006081 and from KEGG species Mycobacterium tuberculosis type Metabolic Pathways curator KEGG RVOT7T6lIC 10 RV0761C 71 RVO0761C 120 RV0761C 350 RYOFSLC 561 RV1862 10 The format has these required features The first line contains three parenthesized assignments for species type and curator In the example just above the annotation file created for budding yeast from the flat text file maintained by SGD for the Gene Ontology project and available both at their web site and at GO s shows three yeast ORFs annotated for biological process with respect to GO as described above Following the mandatory title line there are one or more annotation lines each with the form canonicalName ontologyTermID Once loaded this annotation along with the accompanying ontology can be assigned to nodes in a Cytoscape network For this to work the species type of the node must exactly match the species named on the first line of the annotation file The canonicalName of your node must exactly match the canonicalName present in the annotation file If you don t see the expected results when using this feature of Cytoscape check this again as getting either of these wrong is a common mistake 169 Cytoscape User Manual Load
156. ou can select only 3 5 attributes for each import 6 Press Import Import Network and Name Mapping Files 1 Download name mapping files Mapping files are available at http chianti ucsd edu kono genenamemap ping html In this tutorial we are going to use dictionary no prefix zip which 1s a file set without prefixes for each gene names Unzip the archive 158 Cytoscape User Manual 2 Load sample network file Open network import dialog from File gt Import gt Network multiple file types Then click URL radio button and import Human Protein Protein Rual et al Subnetwork for tutorial 3 Open attribute table import dialog from File gt Import gt Attribute from Table 4 Select human dic_cyto txt as the input file 5 Check Show Text File Import Options and click Transfer first line as attribute names checkbox lt listitem gt Uncheck Show Text File Import Options and check Mapping Options lt listitem gt lt listitem gt Select EntrezGene as Primary Key lt listitem gt lt listitem gt Right click on EntrezGene column name and set the type to String lt listitem gt lt listitem gt Do the same for HGNC lt listitem gt lt listitem gt Right click on Other Aliases and select List as the data type lt listitem gt lt listitem gt Check Other Aliases as Alias under Alias checkboxes lt listitem gt lt listitem gt Now the Table Import dialog looks like the following scree
157. ove were generated in this manner The available network views are also arranged as multiple overlapping windows in the network view window You can maximize minimize and destroy network views by using the normal window controls for your operating system Arrange Network Windows When you work on multiple networks you can arrange the network view windows from View Arrange Network Windows You can re arrange the network location by these commands META Select Layout Plugins Help Hide Control Panel Cytost Hide Data Panel Show Results Panel EL Show Graphics Details X5 Open VizMapper Arrange Network Windows Cascade YALO4OC Horizontal mom Vertical YPRILAW Y L1 Q YGLOOSC MEGA Select Layout Plugins Help Hide Control Panel Cyto Hide Data Panel Show Results Panel Reif child chi Show Graphics Details Open Viz Mappe r Arrange Network Windows Cascade Tiled Horizontal Vertical 19 Cytoscape User Manual 1 mmm The Network Overview Window The network overview window shows an overview or bird s eye view of the network It can be used to navigate around a large network view The blue rectangle indicates the portion of the network currently displayed in the network view window and it can be dragged with the mouse to view other portions of the network Zooming in will cause the rectangle to appear smaller and vice versa EB EBEN Ceaz
158. p np id nam result result strip if result isa isa or result partof partof print gt gt sys stderr meaningless term np np s np np result else print result if len sys argv 2 print usage np np s someFile xml np np sys argv 0 172 Cytoscape User Manual sys exit inputFilename sys argv 1 print gt gt sys stderr reading np np s np np inputFilename text open inputFilename read print gt gt sys stderr Tread np np d characters np np len text regex lt oo term PARE O termo cregex pre compile regex re DOTALL matches newlines m pre findall cregex text print gt gt sys stderr number of go terms np np d np np len m regex2 goraccession GO go accession go name 7 go name cregex2 re compile regex2 re DOTALL regex3 lt go isa s rdf resource http www geneontology org go GO s gt cregex3 re compile regex3 re DOTALL regex4 lt go part of s rdf resource http www geneontology org go GO s cregex4 re compile regex4 re DOTALL goodElements 0 badElements 0 print curator GO type all EOL tern ome m2 re search cregex2 term ir m2 goodElements 1 id mZ qroup 1 name m2 group 2 Lea TS 7 m3 re findall cregex3 term for Det an mes isalDs append ref m4 re findall cregex4 term p
159. pe This option also subsumes the previous resource plugin option You may specify a class name that identifies your plugin and the plugin will be loaded if the plugin is in Cytoscape s CLASSPATH For example assuming that the class MyPlugin can be found in the CLASSPATH you could specify the plugin like this cyto scape sh p MyPlugin class A final means of specifying plugins is to specify a file name whose contents contain a list of plugin jar files 21 Cytoscape User Manual P props lt file gt This option specifies Cytoscape properties Properties can be specified either as a properties file in Java s standard properties format or as individual properties To specify individual properties you must specify the property name followed by the property value where the name and value are separated by the sign For ex ample to specify the defaultSpeciesName cytoscape sh P defaultSpe ciesName Human If you would like to include spaces in your property simply enclose the name and value in quotation marks cytoscape sh P default SpeciesName Homo Sapiens The property option subsumes previous op tions noCanonicalization species and bioDataServer Now it would look like cytoscape sh P defaultSpeciesName Human P noCanonic alization true P bioDataServer myServer V vizmap lt file gt This option specifies a visual properties file All options described above including plugins can be loaded from the GUI once
160. pe URL i Select from pull down menu e Drag amp Drop URL from Web Browser Importing networks from URL addresses has an important caveat Because Cytoscape determines file type primarily not exclusively by file extension it can have trouble importing networks with URLs that don t end in a human readable file name If Cytoscape does not recognize a meaningful file name and extension in the URL it will attempt to guess the type of file based on MIME type If the MIME type is not recog nizable to any of our import handlers then the import will fail Another issue for network import is the presence of firewalls which can affect which files are accessible to a computer To work around this problem Cytoscape supports the use of proxy servers To configure the proxy server go to Edit Preferences Proxy Server This is further described in the Preferences chapter Import Free Format Table Files Introduced in version 2 4 Cytoscape now supports the import of networks from delimited text files and Excel workbooks using Edit Import Network from Table Text MS Excel An interactive GUI allows users to specify parsing options for specified files The screen provides a preview that shows how the file will be parsed given the current configuration As the configuration changes the preview updates automatically In addition to specifying how the file will be parsed the user must also choose the columns that represent the Source no
161. ped with the plugin to get started To use the old filters go to Select Use Old Filters You will see a filters window which initially looks like the following 141 Cytoscape User Manual Use Filters Manage Filters There is no filter currently selected To edit a Filter select it from the Available Remove selected Filte Filters list IF the list is empty you can create a new Filter with the Create new Available Filters filter button Select All Filter Node canonicalName YL Node canonicalName YC Manage Filters String Pattern Filter Create new filter Remove selected filter Available Filters Filter Name e canonicalName yL Select All Filter Node canonicalName YL Select graph objects of type Node y Mode canonicalMame YC with a value for text attribute canonicalName v that matches the pattern YL Apply selected Filter There are three panels in the Filters window e The right hand panel An existing or newly created filter can be edited in this area Each filter type has its own user interface for editing The lower left panel All available filters are shown in this list Initially this list will contain only sample filters but as you create more they will be added here The upper left panel Pressing the Create new filter button adds a filter to the Available Filters box and the Remove selected filter b
162. ple installing the MCODE plugin will automatically result in new menu options such as Plugins MCODE Start MCODE Themes Some groups of plugins have been released in a single bundle called a Theme Installing it will get you the functionality provided by all of the plugins listed within the theme To see available themes just look under the Theme heading under Available for Install Note that once a theme is installed updates to the included plugins will only be installed when the entire theme has been released with a newer version If a theme has been installed none of the plugins may be installed or deleted separately Troubleshooting e If an installation error appears automatic installation of the plugin may not be supported To manually install the plugin go to the Cytoscape plugins page http cytoscape org plugins php scroll down to 149 Cytoscape User Manual find the plugin click on the appropriate link to download the file and then save it in the Cyto scape plugins folder on your hard drive Cytoscape will require a restart in order to load the manually installed plugin f the plugin does not appear in the Currently Installed folder of the Plugin Manager then Cytoscape was unable to load the plugin Your command line will display the error message generated Delete Existing Plugins To delete an existing plugin or theme go to the Plugin Manager at Plugins Manage Plugins click on the appropriate plugin
163. ption of Align Options 79 Cytoscape User Manual Vertical Align Top The tops of the selected nodes are aligned with the top most node Vertical Align Center The centers of the selected nodes are aligned along a line defined by the midpoint between the top and bottom most nodes Vertical Align Bottom The bottoms of the selected nodes are aligned with the bottom most node Horizontal Align Center The centers of the selected nodes are aligned along a line defined by the midpoint between the left and right most nodes Horizontal Align Right The right hand sides of the selected nodes are aligned with the right most node Vertical Distribute Top The tops of the selected nodes are distributed evenly between the top most and bottom most nodes which should stay stationary Vertical Distribute Center The centers of the selected nodes are distributed evenly between the top most and bottom most nodes which should stay stationary Vertical Distribute Bottom The bottoms of the selected nodes are distributed evenly between the top most and bottom most nodes which should stay stationary Horizontal Distribute Left The left hand sides of the selected nodes are distributed evenly between the left most and right most nodes which should stay stationary Horizontal Distribute Center The centers of the selected nodes are distributed evenly between the left most and right most nodes which should stay stationary Horizontal Dist
164. re the gene is stored may be used to refer to a gene e g protein accession numbers from Swiss Prot If one data source 40 Cytoscape User Manual uses the formal name while a different data source used a common name or identifier then Cytoscape must figure out that these two different names really refer to the same biological entity Cytoscape has two strategies for dealing with this naming issue one simple and one more complex The simple strategy is to assume that every data source uses the same set of names for every object If this is the case then Cytoscape can easily connect all of the different data sources To handle data sources with different sets of names as is usually the case when manually integrating gene information from different sources Cytoscape needs a data server that provides synonym information see the chapter on Annotation A synonym table gives a canonical name for each object in a given organism and one or more recognized synonyms for that object Note that the synonym table itself defines which set of names are the canonical names For example in budding yeast the ORF names are commonly used as the canonical names If a synonym server is available then by default Cytoscape will convert every name that appears in a data file to the associated canonical name Unrecognized names will not be changed This conversion of names to acommon set allows Cytoscape to connect the genes present in different data sources e
165. reputation will not be affected by problems that might be introduced by others 175 Cytoscape User Manual Finally software patents pose a constant threat to the existence of any free program We wish to make sure that a company cannot effectively restrict the users of a free program by obtaining a restrictive license from a patent holder Therefore we insist that any patent license obtained for a version of the library must be consistent with the full freedom of use specified in this license Most GNU software including some libraries is covered by the ordinary GNU General Public License This license the GNU Lesser General Public License applies to certain designated libraries and is quite different from the ordinary General Public License We use this license for certain libraries in order to permit linking those libraries into non free programs When a program is linked with a library whether statically or using a shared library the combination of the two is legally speaking a combined work a derivative of the original library The ordinary General Public License therefore permits such linking only if the entire combination fits its criteria of freedom The Lesser General Public License permits more lax criteria for linking other code with the library We call this license the Lesser General Public License because it does Less to protect the user s freedom than the ordinary General Public License It also provides other free software
166. rial is to learn how to create a new Visual Style and set some default values Step 1 Load a sample network From the main menu select File gt Import gt Network Multiple file types and select sampleData galFiltered sif Step 2 Open the VizMapper Select the View Open VizMapper menu option or select the VizMapper icon in the main button bar or click on the VizMapper tab in the Control Panel at the left of the screen You will now see a VizMapper Main Panel as shown below 111 Cytoscape User Manual Im Ty Network VizMapper Editor H b Current Visual Style Defaults Visual Mapping Browser 4 a Y Node Visual Map gt Node Label ID Y Unused Properties Node Color Node Border Color Node Shape Node Sire Node Width Node Height Node Fort Face Node Font Size KI Node Label Color Step 3 Create a new visual style Click the Options button and select Create new visual style Then enter a name for your new visual style when prompted You will see an empty visual style in the VizMapper Main Panel as shown below 112 Cytoscape User Manual Current Visual Style Tutorial V51 HH Defaults Visual Mapping Erowser Y Unused Properties Node Color Double Click to cre Node Border Color Double Click to cre Mardo Share Meanbh loai lirl te rro Since no mapping is set up yet all visual attributes are listed in the Un
167. ribute Right The right hand sides of the selected nodes are distrib uted evenly between the left most and right most nodes which should stay station After Description of Stack Description of Stack Options 0 00 Vertical Stack Left EE stacked below top most node with the left hand sides of the selected nodes aligned Vertical Stack Center Vertically stacked below top most node with the centers of selected nodes aligned Vertical Stack Right Vertically stacked below top most node with the right hand sides of the selected nodes aligned Horizontal Stack Top Horizontally stacked to the right of the left most node with the tops of the selected nodes aligned Horizontal Stack Center Horizontally stacked to the right of the left most node with the centers of selected nodes aligned Horizontal Stack Bottom Horizontal Stack Center Horizontally stacked to the right of the left most node with the bottoms of the selected nodes aligned 80 Cytoscape User Manual Edge Handles This is a little known feature If you select an edge and then Ctrl left click on the edge an edge handle will appear This handle can be used to change the shape of the line To remove a handle simply Ctrl left click on the handle again Straight Edge Smooth Edge Two other options under Select gt Edges provide further control Smooth Selected Edges turns an edge consisting of line segments into a smoothed bezier curve and Straighten S
168. rom the list and press Apply amp e GERT YEROLAC YGL106W YNLI16M 123 Cytoscape User Manual 9 Open Default Appearance Editor again Click NODE_OPACITY and set opacity to 0 YGL106W 10 Double click Node Custom Graphics 2 in the ViaMapper panel and create new Discrete Mapping Set controlling attribute name to Degree 11 For degree value 1 set a Custom Graphics 12 Open Default Appearance Editor Click VODE CUSTOM GRAPHICS POSITION 2 and move the position from the center 13 Apply Force Directed Layout Now you can see all leaf nodes have two Custom Graphics Node Visual Mapping Node Custom Graphics 2 Degree Mapping Type Discrete Mapping Users kono D c 14 Double click Node Custom Graphics 3 in the VizMapper panel and create new Continuous Mapping Set controlling attribute name to Degree 15 Set a Custom Graphics for nodes with degree grater than 10 124 Cytoscape User Manual f f Continuous Editor for Node Custom Graphics 3 Continuous Mapping for Node Custom Graphics 3 v A 10 00000 Degree Range Setting 101 Min Max 16 Open Default Appearance Editor and modify VODE CUSTOM GRAPHICS POSITION 3 17 Edit default appearance for better look Now the network looks like the following 125 Cytoscape User Manual Advanced Topics Editing Discrete Mappings From version 2 5 several utility functions are available for Discrete Mappings You can use those
169. rotein is identified by its IPI number IPI 1s the International Protein Index which maintains cross references to the main databases for human mouse and rat proteomes The second sample contains biological process annotation and each protein is identified by its NP RefSeq number These two naming systems IPI and RefSeq are two of many that you can use to define canonical names when you run Cytoscape For budding yeast it is much easier the yeast community always uses standard ORF names and so Cytoscape uses these as canonical names For human proteins and genes there is no single standard The solution for those working with human genes or proteins is once you have downloaded the annotations file to 1 Decide which naming system you want to use 2 Download ftp ftp ebi ac uk pub databases GO goa HUMAN xrefs goa This cross reference file when used strategically allows you to create Cytoscape compatible annotation files in which the canonical name is the one most meaningful to you 3 Examine xrefs goa to figure out which column contains the names you wish to use 4 Make a very slight modification to the python script described below and then 5 Run that script supplying both xrefs goa and that annotation file as arguments Here are a few sample lines from xrefs goa SE O00115 IPI00010348 ENSP 0 0000222219 NP_001366 SE O00116 IPIO0010349 ENSP00000324567 ENSP00000264167 SE OO0TZ4 JIEIOO00TOJ53 ENSP00000265616 ENSP00000322580 1
170. s Text File Import Options Delimiter Preview Oprions Tab Comma Semicolon Space Other Show all entries in the file 08 Show first 100 entries Attribute Names Network Import Options Transfer first line as attribute names Start Import Raw 1 Comment Line Default Interaction na Reload You can select several options by checking the Show Text File Import Options checkbox e Delimiter You can select multiple delimiters for text tables By default Tab and Space are selected as delimiters e Preview Options When you select a network table file the first 100 entries will be displayed in the Preview panel To display more entries change the value for this option If you want to show all entries in the file select Show all entries in the file You will need to click the Reload button to update the Preview panel e Attribute Names e Transfer first line as attribute names Selecting this option will cause all edge attribute columns to be named according to the first data entry in that column e Start Import Row Set which row of the table to begin importing data from For example if you want to skip the first 3 rows in the file set 4 for this option e Comment Line Rows starting with this character will not be imported This option can be used to skip comment lines in text files e Network Import Options If the Interaction Type is set to Default Interaction the value here will be used as the interaction type for all e
171. s plugins in the plugins directory See the Command Line chapter for more detail In Windows it is also possible to directly double click the jar file to launch it However this does not allow specification of command line arguments such as the location of the plugin directory When you succeed in launching Cytoscape a window will appear that looks like this captured on Mac OS 10 4 Saaana ED aR En Edge hk Maiti ch I PM Webaren te Cytoncage 2 5 Right chek diag ro Note on Memory Consumption For users interested in loading large networks the amount of memory needed by Cytoscape will increase Memory usage depends on both number of network objects nodes edges and the number of attributes Here are some rough suggestions for memory allocation Suggested Memory Size Without View Number of Objects nodes edges Suggested Memory Size 0 70 000 512M default 70 000 150 000 800M Suggested Memory Size With View Number of Objects nodes edges Suggested Memory Size 0 20 000 512M default 10 Cytoscape User Manual 20 000 70 000 SOOM Overall Memory Size for Cytoscape To increase the maximum memory size for Cytoscape you can specify it in a file residing in the same directory as the Cytoscape executable called Cytoscape vmoptions with one option per line and lines separated by linefeeds The last line must also be followed by a linefeed The one exception to th
172. scape Plugin Manager Once installed these web service clients will be centrally accessible via the same steps defined above e File gt Import gt Network from web services Import Attributes from External Database Some of the web service clients can import attributes from external databases BioMart client is an example You can install it from Plugin Manager Example 1 Import Additional ID Sets and Annotations from BioMart 4 eoe Biomart Web Service Client l Q uery biossssmart ed Data Source ENSEMBL 48 GENES SANGER Saccharomyces cerevisiae genes SGD1 01 7 Key Attribute Attribute IDO Data Type l Ensembl Gene ID s Available attributes feature page Interpro ID interpro e m7 n x E feature page Interpro Short Description interpro short description M feature page PDB ID pdb M feature page PFAM ID pfam LA fea ID e El fea in EJ feature page RefSeq Peptide ID refseg_peptide fe eature page 5gd sgd gt e eatur e pat a Ki LU nal ion 1 ai j 1510 nal dom i i kd T Reset Cancel Import Load a network In this example we use galFiltered sif in sampleData directory e File gt Import gt Import Attributes from BioMart Select Data Source Since galFiltered sif is a yeast network select yeast dataset 61 Cytoscape User Manual For Key Attribute section select D for Attribute and Data Type shou
173. se samples to understand how Visual Styles change appearence of a network The following is a list of network views based on sample styles applied to galFiltered sif network 93 Cytoscape User Manual 94 Cytoscape User Manual ih e e e e i e z ki P E din S ex e i D D L a i F gt E e e gt e BW a 9 h E K Ka E di i sz Tl kv P gt e e o e e EN E The VizMapper can be accessed by going to View gt Open VizMapper or by clicking on the VizMapper 1 C O n Also starting in Cytoscape 2 5 direct access to the VizMapper s provided via a tab on the Control Panel at the left hand side of the screen formerly known as CytoPanel 1 95 Cytoscape User Manual Introduction to the VizMapper User Interface As of Cytoscape 2 5 the VizMapper has undergone a complete interface redesign There are three types of components in the new VizMapper 1 Main Panel Control Panel fe Network VizMapper Editor Filters Current Visual Style Sample3 Defaults Visual Mapping Browser Q DIAMOND PARALLELOGRAM P Node Tooltip canonicalName Y Node Color gal4RGexp Mapping Type Continuous Mapping Graphical View Y Edge Visual Mapping Y Edge Color interaction Mapping Type Discrete Mapping pd pp This panel allows you to create delete view switch between different visual styles using the Current Visual Styl
174. ser Manual Step 7 Choose a mapping type Set the Continuous Mapping option as the Mapping Type This automat ically creates a default mapping Y Node Color gallRGexp Mapping Type Continuous Mapping Graphical View Step 8 Define the points where colors will change Double click on the black and white gradient rectangle next to Graphical View to open the Color Gradient Mapper Click and drag one point to 1 or type the value in the Range Setting box Set the second point to 2 000 Gradient Editor for Node Color Continuous Mapping for Node Color lt y VD 1 0000 2 0000 Min 2 426 gal 1RGexp Max 2 058 Range Setting Min Max Add Delete ES Step 9 Define the colors between points Double click on the leftmost triangle facing left and a color palette will appear Choose a shade of yellow and click OK Double click on the triangle at 1 and set the color white For triangle at 2 set its color to red Set the rightmost triangle to black 8008 Gradient Editor for Node Color Continuous Mapping for Node Color il V 1 0000 2 0000 Min 2 426 gal 1RGexp Max 2 058 Range Setting Min Max Add Delete ES The color gradients will immediately appear in the network window All nodes with a gall RGexp value less than 1 will be set to yellow and all nodes with a gallRGExp value greater than 2 will be black Ad ditionally all values between 1 and 2 will be painted with a white red color gradient
175. sing white space will still be read The NNF format is a very simple format that unlike SIF allows the optional assignment of single nested network per node No other node attributes can be specified There are only 2 possible line formats A node node contained in a network network node 2 nodes linked together contained in a network network nodel interaction node2 If a network name first entry on a line appeared previously as a node name in columns 2 or 4 the network will be nested in the node with the same name Also if a name that has been previously defined as a network by being listed in the first column later appears as a node name in columns 2 or 4 the previously defined network will be nested in the node with the same name In summary any time a name is used as both a network name and a node name this implies that the network will be nested in the node of the same name Additionally comments may be included on all lines Comments start with a hash mark and continue to the end of a line Trailing comments after data lines and entirely blank lines anywhere are also permissible Please note that if you load multiple NNF files in Cytoscape they will be treated like a single long concat enated NNF file If you need to embed spaces tabs or backslashes in a name you must escape it by pre ceding it with a backslash so that e g an embedded backslash becomes two backslashes an embedded space a backslash followed
176. squares by changing the node shape visual attribute A network attribute is any data attribute associated with a node or an edge For example each edge in a network may be associated with a label such as pd protein DNA interactions or pp protein protein interactions e A visual mapper maps network attributes to visual attributes For example a visual mapper can map all protein DNA interactions to the color blue and all protein protein interactions to the color red Cytoscape allows a wide variety of visual attributes to be controlled These are summarized in the tables below Visual Attributes Associated Description with Nodes Node Shape The shape of the node Node Fill Color The color of the node Node Opacity The opacity of the color of the node Allows for transparency 99 Cytoscape User Manual Node Border Color The color of the border of the node Node Border Opacity The opacity of the color of the border of the node Allows for transpar ency Node Line Style Ostensibly the type of line used for the border of the node This is not currently functional Node Line Width The width of the node border Node Font Face The font used for the node label Node Font Size The size of the font used for the node label Node Label The text used for the node label Node Label Color The color of the node label Node Label Opacity The opacity of the color of the node label Allows for transparency Node
177. ssues in Cytoscape ccccccece cence cence cence eens eases eens eases ene eaeneeeeneeseaeneeas 40 Node amd Baste Atti Ue B ooo parses sera 41 Cytoscape Attribute File Format 4 Import Attribute Table FCS rescore e di 44 Attribute Functions and Equations oooocccocconcncnnonnononnoncnnonnnnonnononnn nro nono eens eases eeeeseneeaeeseneeaeneees 48 A oo 48 Loading Gene Expression Attribute Matrix Data essssssssesssesssnensnenenennenensnenenn een nenn 52 Data File Formal ER m 52 Celer TPO WN Sst cet ee een 53 AVVO te Example scr D o oS 53 Detailed file format Advanced user 54 Importing Networks and Attributes from External Databases esee 55 Web Service Client Manaser ae ee 55 Ce AAA ee een 56 Cytoscape User Manual Example 1 Retrieving Protein Protein Interaction Networks from IntAct sususe 56 Example 2 Retrieving Protein Protein Interaction Networks from NCBI Entrez Gene SEI Example 3 Retrieving Pathways and Networks from Pathway Commons 58 Future DIT CC ONS ee eier ie 61 Import Attributes trom External Database i ete elle ie 61 Use Multiple Services EE ee lan 64 Nayisat on and Layout as esperes oe beta AS der a law techie dente aati ease Put 66 Basic Network INAayTELIOTE see ine 66 Other Mouse EE 67 Automatic Layout Alcon PiS seien 68 Manual Dy UE one a EA JA Node Movement and Place mentido 81 VISUAL S
178. string representation of the current date 50 Cytoscape User Manual Pitfalls The possibly biggest problem is the referencing of other attributes that have null values This is not allowed and leads to errors In order to mitigate this problem we support the following optional syntax for attribute references attribName default Value The interpretation is that if attribName is null then the default value will be used otherwise the value of the referenced value will be used instead N B the referenced attribute must still be a defined attribute and not an arbitrary name The other potential problem is when there are circular attribute reference dependencies Circular dependencies will be detected at formula evaluation time and lead to a runtime error Useful Tips When working with formulas it can be very helpful to open the Cytoscape Error Console Formula evaluation errors will be logged there The Formula Builder In order to ease the creation of formulas as well as to facilitate discovery of built in functions we provide a formula builder in our attribute browser After selecting a non list attribute cell you can invoke it by C l 1 C k i n g O n fe This should bring up the Formula Builder which looks like this Creating a formula for gallRGexp Call with LOG argument base Next Argument f Degree el or Apply to Current cell only FK MN Ok Cancel e The Formula Builder is a us
179. sual appearance of your network is easily customized For example you can e Specify a default color and shape for all nodes 81 Cytoscape User Manual Deu Apporornce for dau HODE ALE COLOR HODE BORDER COLOR Lack Nade With Heigl Add any photo image graphics on the nodes 82 Cytoscape User Manual Heat shock cognate 71 kDa Esl rogen receptor protein Transcription factor AP 1 1sitional endoplasmic reticulum ATPase Breast cancer type 1 susceptibility protein 83 Cytoscape User Manual Spa aia sesi dir ark u pirja YNL301C YNL216W YBRO93C tros Tred Tyee 2 YDR171W YIL133C YHR174 YOL127W pit YGR254W Ty 11 Tepes Tyee B Type 5 Twpe 1 Typed p P iM Tread Feta 3 Tess p pa Type 1 Tige Z 84 Cytoscape User Manual e Use specific line types to indicate different types of interactions Encode specific physical entities as different node shapes 85 Cytoscape User Manual D aming ac d oxidase Nn dinn Z oxocpentanga gt C D Ornithine 2 e Set node sizes based on the degree of connectivity of the nodes You can visually see the hub of a net work 86 Cytoscape User Manual e or set the font size of the node labels instead 87 Cytoscape User Manual e Set node widths and heights based on label size 88 Cytos
180. t Import Row Comment Line Reload Freviem Legend galExpOata pv als Key Attribunres TPROGZ2W S GENE a COMMON 11 G galdRG a gal amp R M galit YPROROW THROSIW CONG 0034 0 111 0 304 375720401 YHR 12 4W NDTBEO 0 090 0 007 0 348 271480001 O YPRIOZE YKL181W PRS1 0167 0 233 0 112 6 27120e 03 YPR110 YGRO72W UPF3 0 245 0 471 0 787 4 104508 04 YPR113W YHLO20C OPI 0 174 0 015 0 151 140160e 04 k YGRIASW YGR145W D 387 0 577 1 088 5 378200 03 YPR119W YGLOA41C YGLOA1C 0 285 Dog 0 103 4 AB050r 04 YPR124W YGR2 18W CRMI 0 018 0 001 0 018 amp i3810 0 YPR145W i a A De Tan wT F YPR 167C ober ef matched Primary Kew and Key Aitrikarbe pair 8 First lOO entries are loaded for preview File Sine 415 Fayed im port di Cantal d Sample Attribute Table 1 AAC3 YBRO85WIANC3 S000000289 AAT2 YLRO27CIASP5 S000004017 BIK1 YCLO29CIARMSIPAC 14 S000000534 The attribute table file should contain a primary key column and at least one attribute column The maximum number of attribute columns is unlimited The Alias column is an optional feature as is using the first row of data as attribute names Alternatively you can specify each attribute name from the File Import gt Attribute from Table text MS Excel user interface 44 Cytoscape User Manual Basic Operation The user interface of the Import Attributes from Table window is similar to
181. t can be defined by choosing attributes one at a time in the Attribute Filter comboBox and clicking the Add button Note that in the comboBox each attribute has a prefix either node or edge denoting what type of attribute it is After add button is clicked a widget depended on the item selected will be added to the definition panel If the attribute type is text based or String the widget will be a indexed text box widget if numeric attribute the widget will be a range slider both are shown below Fo amp Control Panel Attribute Filter Inode gal4AGsig Advanced annotation Date Not 20010119 3 AND galncsig wt a For each widget the name of the attribute it represents is on the left A NOT checkbox gives the option to get the negation of selection for the widget There is a trash can icon on the right Clicking on the trash can icon will delete the widget In this way the filter definition can be modified after it is defined Note that if more than one widget is added on the filter definition panel the relationship between them is AND by default This relationship can be changed to OR by selecting the OR relation in Advanced Panel 138 Cytoscape User Manual The Advanced panel can be opened by clicking on the plus sign Advanced Save 4 Session Global Relation f AMD OR Negation 7 There are three rows in the advanced panel 1 The first row labeled Save The two checkbo
182. t ead Ee dE 154 Node Name Map pi cose ora terae oe Coo reboot tian osea stica Mi ota ott dia Lacs uae dd 157 Import Ontoloby ee EE 161 Custom Annotation Files for Ontologies Other than GO for Advanced Users 162 A Bela 165 Addine or Removile Enke tb css 166 Use LinkOut trom Aibute Browser anna ee eu tinet 167 Cytoscape User Manual IC KNOW HD TEN e 167 Appendix A Old Annotation Server Format 168 Building your own annotation files esses emen mene ene emen eene 168 Load Data mo GVO SCAG ee ende ee teren 170 Getting and Reformatting GO Data zelnen an ers ae 170 I COUP SCO cupio rt temp So EU ML a ee rasen 172 Appendix B GNU Lesser General Public License eere oorr cet 175 Appendix C Increasing memory for Cytoscape anne anne 181 How to increase memory for Cyan een 181 Changing memory allocations on Windows Mac and Linux machines ususuese 181 Cytoscape User Manual This document 1s licensed under the Creative Commons license 2006 Authors The Cytoscape Collaboration The Cytoscape project is an ongoing collaboration between University of California at San Diego i Institute for Systems Biology i Memorial Sloan Kettering Cancer Center E Institut Pasteur i Agilent Technologies E University of California at San Francisco Funding for Cytoscape is provided by a federal grant from the U S National Institute of General Medical Sciences NIGMS of the National Inst
183. t sif Or you can specify a network as a URL cytoscape sh N http ex ample com myNet sif h help This flag generates the help output you see above and exits This flag prints the version number of Cytoscape and exits S session lt file gt This option specifies a session file to be loaded Since only one session file can be loaded at a given time this option may only specified once on a given command line The option expects a cys Cytoscape session file It is customary although not necessary for session file names to contain the cys extension N network file This option is used to load all types of network files SIF GML and XGMML files can all be loaded using the N option You can specify as many networks as desired on a single command line e edge attrs lt file gt This option specifies an edge attributes file You may specify as many edge attribute files as desired on a single command line n node attrs lt file gt This option specifies a node attributes file You may specify as many node attribute files as desired on a single command line m matrix file This option specifies a data matrix file In a biological context the data matrix consists of expression data All data matrix files are read into node attributes You may specify as many data matrix files as desired on a single command line p plugin lt file gt This option specifies a cytoscape plugin jar file to be loaded by Cytosca
184. tgenome org cgi bin loc places the SGD link under the yeast submenu This link will appear in Cytoscape as vain YBRIG4Aj3L Visual Mapping Bypass Use Web Services i Reactome V WormBase worm Array Express HGNC human Ensembl Gene View FlyBase fly KEGG v SGD yeast Entrez MGI mouse Interaction Databases iHOP Other Biological DB Ontology EBI Tools UniProt Search Engines In a similar fashion one can added new submenus The ID string in the URL is a place holder for the node label When the popup menu is generated this marker is substituted with the node label In the above example the generated SGD link for the YIMI protein is http db yeastgenome org cgi bin locus pl locus YIM1 If you want to query based on a different attribute you currently need to specify a different Node Label using the VizMapper For edges the mechanism is much the same however here the placeholders ID1 and ID26 reflect the source and target node label respectively Currently there is no mechanism to check whether the constructed URL query is correct and if the node label is meaningful Similarly there is no ID mapping between various identifiers For example a link to NCBI Entrez from a network that uses ensembl gene identifiers as node labels will produce a link to Entrez using ensembl ID which results in an incorrect link It is the user s responsibility to ensure that the node label that is used as the s
185. th it No ac tual network will be deleted e Go to Nested Network After selecting this the network view of the current node s nested network will be the current network view and have the focus Should a network view for the nested network not exist it will be created 67 Cytoscape User Manual Automatic Layout Algorithms The Layout menu has an array of features for organizing the network visually according to one of several algorithms aligning and rotating groups of nodes and adjusting the size of the network Most of these features are available from plugins that are packaged with Cytoscape 2 3 and above Cytoscape layouts have three different sources which are reflected in the Layout menu yFiles Layouts yFiles layouts are a set of commercial layouts which are provided courtesy of yWorks Due to license re strictions the detailed parameters for these layouts are not available there are no yFiles entries in the Settings dialog The main layout algorithms provided by yFiles are yFiles Circular Layout This algorithm produces layouts that emphasize group and tree structures within a network It partitions the network by analyzing its connectivity structure and arranges the partitions as separate circles The circles themselves are arranged in a radial tree layout fashion This algorithm is available by selecting Layout yFiles Circular i eoe sample ii ipid dde da ao S S m es gt amp SS amp
186. the files and the date of any change c You must cause the whole of the work to be licensed at no charge to all third parties under the terms of this License d If a facility in the modified Library refers to a function or a table of data to be supplied by an application program that uses the facility other than as an argument passed when the facility is invoked then you must make a good faith effort to ensure that in the event an application does not supply such function or table the facility still operates and performs whatever part of its purpose remains meaningful For example a function in a library to compute square roots has a purpose that is entirely well defined independent of the application Therefore Subsection 2d requires that any application supplied function or table used by this function must be optional if the application does not supply it the square root function must still compute Square roots These requirements apply to the modified work as a whole If identifiable sections of that work are not derived from the Library and can be reasonably considered independent and separate works in themselves then this License and its terms do not apply to those sections when you distribute them as separate works But when you distribute the same sections as part of a whole which is a work based on the Library the distribution of the whole must be on the terms of this License whose permissions for other licensees extend to the
187. tifier ID This is the value seen in the leftmost column of the attribute browser This does not change even if the displayed node label changes Select gt Nodes gt From File selects nodes based on node identifiers found in a specified file The file format is simply one node id per line Nodel Node2 Node3 145 Cytoscape User Manual Editing Networks Using Cytoscape s Editor you can build and modify networks interactively by dragging and dropping nodes and edges from a palette onto the main network view window The palette contains a set of shapes for nodes and arrows for edges The shapes on the palette are defined by the current Visual Style with Node Shape and Node Color mapping into the shape and color of a node and Edge Target Arrow mapping into the target arrow of an edge An example of an editor with the palette contained in CytoPanel 1 is shown below a Cytoscape Version 2 5 File Edit View Select Layout Plugins Help i eoe Cytoscape Desktop New Session TI EXY CY 1 E Control Panel da ee Network 0 te Network VizMapper Editor Filters Directed Edge Add a Node b Welcome to Cytoscape 2 5 Right click drag to ZOOM Middle click drag to PAN To edit an existing network just select the Editor tab in CytoPanel 1 To start editing a new network create a new network by going to File gt New Network Empty Network To add a node to a network drag and drop a node shape from th
188. tion filter Topology Filter Topology filter will select nodes based on the properties of its near by nodes neighbors To create a topo logy filter choose the menu item Create new topology filter from the option menu See below 139 Cytoscape User Manual Interaction filter Interaction filters are used to select nodes edges based on the properties of their neighboring edges nodes See below for a node interaction filter 140 Cytoscape User Manual pm Control Panel Interaction Filter Definition Advanced Select Nodes which are the Ww Source W Target of at least one edge which pass the filter Using Old Filters The old filters is the one existed in previous versions of Cytoscape Several types of filters are available Basic filters allow the selection of multiple nodes or edges according to singe attribute data e String filters allow selection of nodes or edges with attributes matching specified text patterns These patterns may include the wildcards and e Numerical filters allow selection of nodes or edges according to numerical attributes and the mathemat ical operators gt and lt Compound filters allow selection based on the application of pre existing filters Topology filters allow selection of nodes with neighbors that match some pre existing filter Boolean filters allow the combination of multiple filters using the AND OR and XOR operators Example filters are ship
189. to the out of memory error please reduce the stack size and try again For more details see How_to_increase_memory_for_Cytoscape Note on Directory Location For the application to work properly all files should be left in the directory in which they were unpacked The core Cytoscape application assumes this directory structure when looking for the various libraries needed to run the application If you are adventurous you can get creative with the SCLASSPATH and or the cytoscape jar manifest file and run Cytoscape from any location you want Quick Tour of Cytoscape When a network is loaded Cytoscape will look something like the image below 12 Cytoscape User Manual sa AQAA e 9 Control Panel ze w Network Nodes Edges Y f TA ar LI zT TE e w t SCH ar x ek ists iL 7 P d d CH 33110 36210 Ze 4 Ka w E a T C i ifs GO F ras D a 5 ae E ey E a Ki d Nm c 4 AC c 00 Ema E BUR a d HA UTE i NT SE EAN AAA zat ES 4x ZA Ce E Vesey T ZB gi Data Panel Ze OBS SSES N Edge Attribute Browser Welcome to Cy1ascape 2 8 0 aght click drag 1a ZOOM Middle click drag ta PAN The main window here has several components The menu bar at the top see below for more information about each menu The toolbar which contains icons for commonly used functions These functions are also available via
190. ual style In this manner you can use control clicking as a kind of stamp to add multiple nodes of the same type to the network Control clicking on a node on the canvas starts an edge with its source at that node Move the cursor and a rubber banded line will follow the cursor As the cursor passes over another node that node is highlighted and the rubber banded line will snap to a connection point on that second node Control click the mouse again and the connection will be established The EDGE TYPE attribute of the edge will be the same as the EDGE TYPE of the edge most recently added defaulting back to the original visual style You can abort the drawing of the edge by control clicking on an empty spot on the palette You can delete nodes and edges by selecting a number of nodes and edges then selecting Edit Delete Selected Nodes and Edges You can recover any nodes and edges deleted from a network by going to Edit Undo However note that this will restore all nodes and edges that were previously deleted from the network not just those deleted by the most recent delete operation Add Interactions SIF Style You can also add interactions by typing SIF Simple Interaction Format style entries Select a network you want to add new interactions 2 Open Editor 147 Cytoscape User Manual 3 Double click space on the network window You will be asked to type interaction in SIF style Try A pp B 4 New interaction appe
191. uch claims this section 179 Cytoscape User Manual has the sole purpose of protecting the integrity of the free software distribution system which is implemented by public license practices Many people have made generous contributions to the wide range of software distributed through that system in reliance on consistent application of that system it is up to the author donor to decide if he or she is willing to distribute software through any other system and a licensee cannot impose that choice This section is intended to make thoroughly clear what is believed to be a consequence of the rest of this License 12 If the distribution and or use of the Library is restricted in certain countries either by patents or by copyrighted interfaces the original copyright holder who places the Library under this License may add an explicit geographical distribution limitation excluding those countries so that distribution 1s permitted only in or among countries not thus excluded In such case this License incorporates the limitation as if written in the body of this License 13 The Free Software Foundation may publish revised and or new versions of the Lesser General Public License from time to time Such new versions will be similar in spirit to the present version but may differ in detail to address new problems or concerns Each version is given a distinguishing version number If the Library specifies a version number of this License which appl
192. ugh the proxy server Other plugins use this capability as well The proxy settings are saved in cyto scape props Each time you click the Update button after making a change to the proxy settings an attempt 1s made to connect to a well known site on the Internet e g google com using your settings For both success and failure you are notified and for failure you are given an opportunity to change your proxy settings If you no longer need to use a proxy to connect to the Internet simply uncheck the Use Proxy checkbox and click the Update button Creating Networks There are 4 different ways of creating networks in Cytoscape 1 Importing pre existing formatted network files 24 Cytoscape User Manual 2 Importing pre existing unformatted text or Excel files 3 Importing networks from Web Service 4 Creating an empty network and manually adding nodes and edges Import Fixed Format Network Files Network files can be specified in any of the formats described in the Supported Network Formats chapter Networks are imported into Cytoscape through the Import Network window which can be accessed by going to File gt Import gt Network multiple file types The network file can either be located directly on the local computer or found on a remote computer in which case it will be referenced with a URL Load Networks from Local Computer By default Cytoscape loads networks from the local computer The Import Networks d
193. ults to 300 render edgeLa If the number of rendered edges equals to or exceeds this number edge labels belThreshold will not be rendered this value defaults to 150 When printing networks or exporting to formats such as PostScript the highest level of detail is always chosen regardless of what is currently being displayed on the screen Force to Display Detail If you want to display every detail of the network regardless of LOD values you can use View Show Graphics Details This option force to display every graphics details If the network is large this option slows down rendering speed Annotation Annotations in Cytoscape are stored as a set of ontologies e g the Gene Ontology or GO An ontology consists of a set of controlled vocabulary terms that annotate the objects For example using the Gene Ontology the Saccharomyces Cerevisiae CDC55 gene has a biological process described as protein bio synthesis to which GO has assigned the number 6412 a GO ID GO 8150 biological process GO 7582 physiological processes GO 8152 metabolism GO 44238 primary metabolism GO 19538 protein metabolism GO 6412 protein biosynthesis Graphical View of GO Term 6412 protein biosynthesis 153 Cytoscape User Manual ao vin process metabolism N primary metabolism biosynthesis 2 Rn d il protein metabolism protein blosynthesis Cytoscape can use this ontology DAG Directed Acyclic Graph to annotate
194. urns the cosine of an angle given in radians Cosh Returns the hyperbolic sine of its argument e Count Returns the number of numeric values in a list Degrees Returns its argument converted from radians to degrees Exp Returns e raised to a specified number Ln Returns the natural logarithm of a number Log Returns the logarithm of a number to a specified base Max Returns the maximum of a group of numbers Median Returns the median of a list of numbers Min Returns the minimum of a group of numbers Mod Calculates the modulus of a number Pi Returns an approximation of the value of m Radians Returns its argument converted from degrees to radians Round Rounds a number to a specified number of decimal places e Sinh Returns the hyperbolic sign of its argument e Sin Returns the sine of an angle given in radians e Sort Calculates the square root of a number Tan returns the tangent of its argument in radians e Trunc Truncates a number String Functions Concatenate Concatenates two or more pieces of text Left Returns a prefix of s string Len Returns the length of a string Lower Converts a string to lowercase Mid Selects a substring of some text Right Returns a suffix of a string e Substitute Replaces some text with other text e Text Format a number using the Java DecimalFormat class conventions 49 C
195. used Properties category From this panel you can create node edge mappings for all visual properties Step 4 Edit default values Open the Default Appearance Editor by clicking on the Defaults graphics window shown below in the VizMapper Main Panel em Default Appearence for Tutorial 45 1 HOOD FLL COLOR WODE SOADER COLOR RO SHAPE 25 0 woor sr HOCE LABEL Font ROL PONT FACE gege re W Lock Mode With binighe l Anpiw Gahw 113 Cytoscape User Manual Step 5 Change the default node shape To set the default node shape to triangles click Node Shape in the Default Visual Properties list A list of available node shapes will be shown Click on the Triangle icon and then click the Apply button The Default Appearance Editor will be automatically updated You can edit other default values by clicking on visual attribute names on the list In the example shown below the node shape is set to Triangle while the node color is set to blue e Default Appsarsnza for Tutorial 451 HOOT FRL COLDA Font ROL PONT FACE Lee Edge Gab W Lock Mode With ei gh Apply Step 6 Apply your settings When you finish editing click the Apply button at the bottom of the editor Your new Visual Style will be applied to the current network as shown below ELI Cytoscape Desktop New Session je E Q amp Q1 G E Ag see B Control Panel i aaa galFiltered sif iy weno
196. ute file names often use the suffix noa while edge attribute file names use the suffix eda Cytoscape re cognizes these suffixes when browsing for attribute files Node and edge attributes may be loaded at the command line using the n and e options or via the File Import menu When expression data is loaded using an expression matrix it is automatically loaded as node attribute data unless explicitly specified otherwise Node and edge attributes are attached to nodes and edges and so are independent of networks Attributes for a given node or edge will be applied to all copies of that node or edge in all loaded network files re gardless of whether the attribute file or network file is imported first Note In order to import network attributes in Cytoscape 2 4 please go to File gt Import gt Attribute from Table text MS Excel or encode them in an XGMML network file see Supported File Formats for more details Detailed file format Advanced users Every attribute file has one header line that gives the name of the attribute and optionally some additional meta information about that attribute The format is as follows attributeName class JavaClassName The first field 1s always the attribute name it cannot contain spaces If present the class field defines the name of the class of the attribute values For example java lang String or String for Strings java lang Double or Double for floating point values
197. utton deletes the currently selected filter Creating Filters Clicking the Create new filter button allows you to select a type of filter to create as shown below 142 Cytoscape User Manual Filter Creation Dialog Filter types Filter Type Description Numeric Filter Select nodes or edges based on the String Filter value of a numeric attribute Topology Filter Boolean Meta Filter Node Interactions Edge Interactions The important thing to realize when creating a filter is that the filter does not do anything by itself Once created the filter must be applied to the network String Filter Use Filters Manage Filters String Pattern Filter Create new Filter Remove selected Filter Available Filters Filter Name Mode canonicalName Select All Filter Node canonicalllame YL Node canonicalName YC Mode canonicalName Select graph objects of type Node with a value for text attribute canonicalName that matches the pattern Apply selected Filter The String Filter allows you to filter nodes or edges by a given text attribute of your current loaded network Search terms are entered in the text box at the bottom For example to match any Node whose canonic alName starts with YDL you would select Node canonicalName and then type in YDL The is important as it matches any number of characters after YDL If you want to be more specific and only select no
198. ven if they have different names as long as those names are recognized by the synonym server For this to work Cytoscape must also be provided with the species to which the objects belong since the data server requires the species in order to uniquely identify the object referred to by a particular name This is usually done in Cytoscape by specifying the species name on the command line with the P option cytoscape sh P defaultSpeciesName Saccharomyces cerevisiae or by editing the properties under Edit Preferences Properties The automatic canonicalization of names can be turned off using the P option cytoscape sh P canonicalizeName false or by editing the properties under Edit gt Preferences gt Properties This canonicalization of names currently does not apply to expression data Expression data should use the same names as the other data sources or use the canonical names as defined by the synonym table Node and Edge Attributes Interaction networks are useful as stand alone models However they are most powerful for answering scientific questions when integrated with additional information Cytoscape allows the user to add arbitrary node edge and network information to Cytoscape as node edge network attributes This could include for example annotation data on a gene or confidence values in a protein protein interaction These attributes can then be visualized in a user defined way by setting up a mappin
199. wrap the label on space characters Cytoscape will not hyphenate words meaning 100 Cytoscape User Manual that if a single word e no spaces is longer than maximum width the word will be printed beyond the maximum width The font used for the edge label The size of the font used for the edge label Edge Tooltip The text of the tooltip that appears when a mouse hovers over the edge Edge Source Arrow Color The color of the arrow on the source node end of the edge Edge Source Arrow Opacity The opacity of the color of the arrow on the source node end of the edge Allows for transparency Edge Source Arrow Shape The shape of the arrow on the source node end of the edge Edge Target Arrow Color The color of the arrow on the target node end of the edge Edge Target Arrow Opacity The opacity of the color of the arrow on the target node end of the edge Allows for transparency Edge Target Arrow Shape The shape of the arrow on the target node end of the edge The color of the edge when selected in the Attribute Browser Edge Line Styles Arrow Types For each visual attribute you can specify a default value or define a dynamic visual mapping Cytoscape currently supports three different types of visual mappers 1 Passthrough Mapper The values of network attributes are passed directly through to visual attributes A passthrough mapper is only used to specify node edge labels For example a passthrough mapper can label all
200. xes Global and Session will determine where the filter is saved By default filters are saved in individual sessions If the Global checkbox is checked the filter will be saved in the global properties file Note also that the prefix of the filter name in the Current Filter dropdown list reflects where it is saved 2 The second row Relation will determine what Boolean operation AND or OR will be applied to each individual widget 3 Negation checkbox If this checkbox is checked the result of the filter will be negated Definition of complex filter In the pull down list of Attribute Filter comboBox there are two sections the top one is the list of attributes the bottom one is the list of previously defined filter Those previously dfined filters can also be used as components of other filters By combinational use of AND OR NOT and pre defined filters filters with arbitary complexity can be defined 3 Apply the filter If a network is small number of nodes or edges less than 1000 the filter will be applied dynamically when a widget is added or any value is adjusted If the network is large then Apply button should be clicked to apply the filter The threshold 1000 by default can be changed by defining a Cytoscape property value dynamicFilter Threshold 4 Other filters In the option menu pulldown there are menu items Create new topology filter Create new Nodelnter action filter and Create new Edgelnterac
201. y remark cvs version Revision 5 49 Term id GO 0000001 name mitochondrion inheritance namespace biological_process 154 Cytoscape User Manual def The distribution of mitochondria including the mitochondrial genome into d synonym mitochondrial inheritance EXACT s_a GO 0048308 organelle inheritance 18 sas GOSO00483 Lr d mitochonderLon distribution Term id GO 0000002 name mitochondrial genome maintenance namespace biological_process def The maintenance of the structure and integrity of the mitochondrial genome is a GO 0007005 mitochondrion organization and biogenesis Default List of Ontologies Cytoscape provides a list of ontologies available in OBO format If an Internet connection is available Cytoscape will import ontology and annotation files directly from the remote source The table below lists the included ontologies Gene Ontology Full This data source contains a full size GO DAG which contains all GO terms This OBO file is written in version 1 2 format Generic GO slim A subset of general GO Terms including higer level terms only Yeast GO slim A subset of GO Terms for annotating Yeast data sets maintained by SGD Molecule role INOH Pro A structured controlled vocabulary of concrete and abstract generic protein tein name family name on names This ontology is a INOH pathway annotation ontology one of a set tology of ontologies intended to be used in pathway data a
202. y Commons Web Service Client Then follow the three step process outlined below 58 Cytoscape User Manual Import Network from Database Import Network From Database gt Data Source Pathway Commons Web Service Client rh Options BRCAI All Organisms i Examples TPS 3 Step 2 Select 1D Step 3 Select Network s Pathways Interaction Networks Pathway Data Source DNA Repair Reactome Double 5trand Break Repair Reactome Homologous Recombination Reactome Homologous recombination r Reactome Details ATM mediated response to D Reactome ATM mediated phosphorylati Reactome BRCAI Recruitment of repair and sig Reactome Aurora A signaling NCI Nature Pathway Interact Homo sapiens BARD signaling events NGI Nature Pathway Interact Signaling by Aurora kinases NCI Nature Pathway Interact Links AndrogenReceptor Cancer Cell Map BRCAL interacting protein 1 RRC Al associated protein 1 BRAPZ NER1 Alar bes BO A 1 enen I Arne UniProt P33398 gt Double click pathway to retrieve RefSeq Protein e Step 1 Enter your search term for example BRCAI e Step 2 Select the protein or small molecule of interest Full details regarding each molecule is shown in the bottom left panel e Step 3 Download a specific pathway or interaction network Downloading Pathways and Interaction Networks In Step 3 you can simply double click on a pathway of interest or click on t
203. yle default exportTextAsShape true maximizeVviewOnCreate false MOTE Changes to these properties are used in the current session ONLY unless otherwise specified below Default Visual Styles Only check this option if you want the current visual styles to be defaults in ALL future cytoscape sessions Your current visual styles are automatically Saved in your Cytoscape session file and won t be lost Make Current Visual Styles Default Default Cytoscape Properties Only check this option if you want the current Cytoscape properties to be defaults in ALL future cytoscape sessions Your current Cytoscape properties are automatically saved in your Cytoscape session file and won t be lost Make Current Cytoscape Properties Default Some common properties are described below Property name Default value Valid values default WebBrowser A path to the web browser on your system This only needs to be specified if Cytoscape can t find the web browser on your system Setting Default Properties It is possible to alter the default properties for Cytoscape Edit the properties via Edit Preferences Properties and check the Make Current Cytoscape Properties Default checkbox This will save the current properties to the cytoscape directory where they will then be applied to all of your Cytoscape sessions from that point on Otherwise Cytoscape will automatically save the properties used in a particular session insi
204. ytoscape User Manual Upper Converts a string to uppercase Value Converts a string to a number Logical Boolean Functions And Returns the logical conjunction of any number of boolean values Not Returns the logical negation of a boolean value Or Returns the logical disjunction of any number of boolean values List Functions BList creates a list of boolean a k a logical or truth values First Returns the first entry in a list FList creates a list of floating point a k a decimal numbers Last Returns the last entry in a list List creates a list of integers a k a whole numbers Nth Returns the n th entry in a list SList creates a list of strings a k a text objects Statistical Functions Largest the kth largest value in a list GeoMean the geometric mean of a set of numbers HarMean the harmonic mean of a set of numbers Mode the mode of a set of numbers NormDist Returns the pdf or CDF of the normal distribution Permut Returns the number of permutations for a given number of objects StDev sample standard deviation Var sample variance Miscellaneous Functions Combin Returns the number of combinations for a given number of objects If Returns one of two alternatives based on a boolean value ListToString Returns a string representation of a list Now Returns a string representation of the current date and time Today returns a

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