MetScape 3.0.2 User Manual
Contents
1. 9 Select a Network Type by selecting one of the following from the dropdown menu e Compound Reaction Enzyme Gene 1 e Compound Reaction 2 e Compound Gene 3 e Compound 4 Note When selecting Compound as the Network Type a dropdown menu appears under Query providing the option of choosing between compounds or genes When any other Network Type is selected the only option is to use compounds genes unless using a selected pathway 10 Click Build Network to query the database and create the network Page 8 of 35 Option 2 Load an experiment file Use to load experimental data to visualize and explore compound networks over time or in varying experimental conditions The input can be an Excel comma or tab delimited file MetScape allows users to load three types of files compound file gene file and concept file Each type is optional e g you can load only compounds only genes only concepts or any combination of the above Compound File The compound data file must meet the following requirements e The first row must be a heading row in which o The columns in the first row are column headings to label the data e All other rows contain experimental data in which o The first column contains KEGG Compound IDs or names o The remaining columns contain experimental data Multiple experimental values are permissible in the same spreadsheet Below is a portion of an example compound file with Compound IDs2. 2 Number of Genes in Network the number of input genes that belong to the concept 3 Direction direction of the change 4 P value the p value for enrichment depletion Page 21 of 35 5 False Discovery Rate the FDR estimated using the method of Benjamini and Hochberg When results are sorted by p value a FDR lt 0 05 is interpreted to mean that approximately 5 of the concepts with lesser or equal p value are false positives TO map a concept on the graph click on the concept name in the Data Panel The concept will then be highlighted in the graph associated nodes turn yellow and associated edges turn red T h pe 7 F i aJ Pe 7 lt a concen Name Number of Enriched Driving Ge Number of Genes in Netw l P va False Discovery R Chondroitin sulfate biodynthesis 24 8 t 0 014 0 101 a Chronic myeloid let pe 76 3o r 0 046 0 203 Citrate cyde TCA cyde 67 a 0 0182 0 103 Colorectal cancer a e eee Complement and coagulation cascades er respons Cyanoamino acd metabolism _ 10 0156 S 101 Node Table e Edge Table r Network Table ii o Filter Concept Filter A subgraph can be created for a given concept The subgraph consists of genes considered to be significant to the concept those genes that drive the concept not all genes in the concept To create a subgraph 4 Select a concept in the Concept F
3. Arachidonic acid metabolism ii C2 1 teroad hormone biosynthesis and metabolism De novo fatty acid biosynthesis Dimethyl branched chain fatty add mitochondrial beta oxdation Di unsaturated fatty acd beta oxidation fe Node Table Edge Table Network Tab Concept Fiter A subgraph can be created for a given pathway The subgraph consists of a subset of nodes from an active network that belong to the selected pathway To create a subgraph 1 Select a pathway in the Pathway Filter tab 2 Click the Create Subnetwork button at the top of the Data Panel make sure you are on the Pathway Filter tab 3 A new graph appears in the graph window This is the subnetwork for the selected pathway Concept filter in the data panel The content of the created or loaded concept file is put into the Concept Filter tab Table Panel Concept Name Number of Enriched Driving Genes Number of Genes in Network 1 4 Dichlorobenzene degradation 21 1 and 2 Methyinaphthalene degradation 25 3 Chloroacrylic acd degradation fis Acute myeloid leukemia 53 lAdherens junction 74 Adipocy tokine signaling pathway 71 Node Table Edge Table Network Table Pathway Filter Concept Fitter Ol os wo N 1 N H 1 Concept Name official name of the concept
4. keep track of the number of downloads Your information will be stored in a secure database and we will not share it with anyone We may send you infrequent e mails about future MetScape releases Note This plugin requires Cytoscape 3 0 to run correctly Page 5 of 35 ENTERING DATA 1 To begin a Cytoscape session with the MetScape plugin first start Cytoscape 2 Choose one of the following methods to get started Option 1 Enter a list of compounds 1 Select Apps gt MetScape gt Build Network from the Cytoscape menu 2 A MetScape tab now appears on the left of the Cytoscape screen 3 Select a species Choices are human rat mouse 4 Manually enter or copy and paste compound ID s or name s and or Entrez gene ID s or symbol s Click Add and enter the appropriate ID type in the popup box Lists of IDs should be separated by spaces lists of compound names should be entered one per line E Cytoscape Desktop New Session s sJ mT File Edit View Select Layout Plugins Help B QQ0 8 Sy 45 Boo Control Panel Jale Build Network Experimental Data pe Compounds none Genes none Concepts none ompounds Input ID may be entered all on one line separated by commas or spaces or one per line Compound names should be entered one per line Adige Remove cer J Reset Genes pa pnput ID Sout Symbol Compound Reaction Enzym
5. 29 Option 2 Expanding a network in a new window Example using Compound Network from Selected Genes che sats sass nna aac oie nopaneneteactuen ue tettest tetteren ttrt atest cennneaaatceceenercesn 31 Collapsing AVE OI crs a sis a een eases Sone Dees ose ese ee ee 32 Creating a subnetwork ssiiscccasaecscersaincisageceseinsdeantertaesgeroerenadnbniescadoarnsudesauiadedaaavecdusntasstananeestuainee detainees 32 Destroying a network seeeenseseensssresesrrresrrerssrreessrereserressrerssrrressrereseteessreresetressrereserersseeresereesseerese 34 SAVING AND REOPENING A SESSION ccccccccccccssssseeeccceecsaeessseeccceessaaeseeececeessuauaeeeceeeessagaaeseseess 34 Saving a SESSION cose ce ctetss see cn catec estevestecc Eanan er NENET ANEAN ENNEN oasis tact deaenneu condemns deceouaeesestnes cecacies 34 Page 2 of 35 REOPENING a SESSION once wi RG A E A SUPPLEMENT METDISEASE AP Poi sicocacoccecesanccinc coteeasanatsucecaute case voinasvuduaducesietiseeadesdcoseipastessdeseeeat Biaeganeaies HOW tO use MetDisease ccc cc cc ecececscccccccccscecececcuccncececeneaeencececenenenenceceteneaeescesetensaencecsseusneasucecs Please note that due to continuous software upgrades the images in this handout may not exactly mimic what you see on the screen Page 3 of 35 OVERVIEW About data sources MetScape is an app for Cytoscape the bioinformatics network visualization tool The app can be used to visualize and interp
6. EGG Pathway 24 0 27898384 5 66198894 0 00167291 0 01625109 up 24158 24450 29711 140547 17046 Glutathione met 24379 24399 24401 24422 25721 Propanoate metdKEGG Pathway 16 0 32105291 7 35380592 0 00265316 0 02122524 up 24158 140547 170465 171155 298 Nitrogen metabqKEGG Pathway 15 0 30373897 6 60362465 up 24379 24399 24401 25721 29242 C5 Branched dibjKEGG Pathway 19 0 26819205 _5 29471153 0 00686636 0 04226683 up 24158 24379 24399 24401 25721 Pyruvate metabqKEGG Pathway 19 0 26689922 5 25234187 0 00714807 0 04226683 up 81829 298942 306198 307858 361 Phenylalanine mKEGG Pathway 21 0 25034932 4 73898475 0 00822755 0 0447139 up _ _ 24368 24401 25721 81683 Antigen processi KEGG Pathway 21 0 2496329 4 71793226 0 00641626 0 044 7139 up 24223 24612 25217 25599 Page 10 of 35 To generate a concept file you can click the LRpath button from MetScape that will take you to the LRpath website Note LRpath performs gene set enrichment testing an approach used to test for predefined biologically relevant gene sets that contain more significant genes from an experimental dataset than expected by chance Sartor et al 2009 To run LRpath you need a Gene Expression file with fold change or log fold change values and p values The Gene Expression file needs to contain all gene records not just those for significant genes LRpath will determine the significant genes from the inpu
7. IEA NCIBI National Center for Integrative Biomedical Informatics MetScape 3 0 2 User Manual An App for Cytoscape National Center for Integrative Biomedical Informatics April 2014 2014 University of Michigan This work is Supported by the National Center for Integrative Biomedical Informatics through NIH Grant 1U54DA021519 01A1 Contents OVER VIEN ec neta eet nee tT eer ee eee ee er ert er err eer ert er 4 POUT data SUC rset sa greece nung avec seca enero sed aceasta ese ns 4 Workflow ire 601 een neni a eee ene ee ee eer er ree 4 Installing Cytoscape and the MetScape app on your local computer cccccceccceeeeceeeeeseeeeeens 5 ENTERING DATA crci a E A E cegesooneaueiauaeauetoatins 6 Option 1 Enter a list of COMPOUNGAS ccccccesscccceeseceecescceeeesececeunececeeusecetsuaecesseneeeessuecetsenecetseges 6 Option 2 Load an experiment file ccc cccccccessececeesscceceesececeeeeceeeenseceeseneceeeeeeceeseusecetseneceseeees 9 VISUALIZATION reee E E E 13 METSCAPE TAB eea A hase EA O E E vasa ae A E E A E A eee 14 RULES USED TO BUILD DIFFERENT NETWORK TYPEG ssssssseeeeeceecceeecessesauaeseessseeseeeeeeeeeeeees 15 DATA PANEL DISPLAY rcer ccc ctacedicans ohne conc convenes A chess oananex E E EE O 16 Choosing attributes provided through MetScape ccccccsssccccssseccccesecceeeeeceeseeseceesuecesseeceesenes 16 Rearranging attributes in the table pa
8. N AET MetScape gt External Links Expand Expand in Existing Network N Preferences 1 Collapse Restore Original Network li r 3 Additional compounds and reactions are network is often redrawn 4 The edges between the original node anq Page 30 of 35 Option 2 Expanding a network in a new window Example using Compound Network from Selected Genes 1 Right click on the compound node you want to expand this node is known as the expansion seed node A menu of options will pop up 2 Select MetScape gt Expand gt Expand in Subnetwork Edit Select Group Nested Networks Expand in Existing Network Expand in Subnetwork Expand Collapse Restore Original Network External Links Preferences 3 Anew network is created in a new window This network includes only the expansion seed compound and its related compounds reactions enzymes and genes depending on the Network Type The original color designations are used when the graph is created in a new window Page 31 of 35 Collapsing a network To collapse a network that is expanded in a current network window 1 Zz Right click on the expansion seed compound node Select MetScape gt Collapse and then e To collapse only the branch expanded from that expansion seed compound select Collapse e To collapse all expa
9. are loaded when initially importing the Compounds file A CID C00219 C00503 CO0187 C0221 Coo0047 C16868 C05122 B p value 0 040982 0 008525 0 030047 0 024311 0 017356 0 004029 0 000312 0 000021 0 000252 0 036583 0 016353 0 000014 C Fold change 1 49 1 53 1 85 2 81 1 03 2 01 1 75 1 2 1 38 1 15 1 07 1 4 D t10 0 477255 0 902665 0 489314 0 86923 0 312654 0 19994 0 002804 0 113069 0 775584 0 139549 0 115421 0 125432 2 From the Apps menu choose MetScape gt Page 25 of 35 E t1_1 0 811411 0 698903 0 029276 0 125056 0 651588 0 379436 0 477482 0 035121 0 198474 0 464563 0 541825 0 275928 F t1_2 0 907349 0 309565 0 314592 0 643666 0 386625 0 374019 0 486432 0 403665 0 490499 0 03 7464 0 8363 0 741933 Animate G t20 0 677623 0 33507 0 705353 0 667656 0 413499 0 06454 7 0 683021 0 76909 0 713089 0 041068 0 829824 0 513364 H t21 0 349178 0 761891 0 064872 0 008175 0 650567 0 325439 0 562158 0 665804 0 756346 0 592104 0 001483 0 90862 l t2 2 0 686365 0 042653 0 340032 0 131301 0 926665 0 605136 0 266456 0 783052 0 96571 0 616224 0 302741 0 5 5 744 Apps 7 Tools Help B a App Manager B T A a Gr MetDisease i Tea JIO Build Network f Select Experimental Data a Animate n562 751 l n 26 1 0 369 0 1 Show Legend Filter By About MetScape Sl a a tS ee ee
10. ation about the network is expressed through visualization e A compound is red in the original network and subsequent subnetworks if it was in the original data loaded into MetScape e A green border surrounding a node represents a significant gene compound e Node size represents the direction of the change Larger nodes represent an increase and smaller nodes represent a decrease in gene metabolite The actual amount of the change is not represented visually e When a node is expanded the edges between the original node and the expanded nodes become blue METSCAPE TAB This tab has options for choosing Network Types the data you entered and more From this tab you can e Select the type of network that you want to build Select Network Type by selecting one of the following from the dropdown menu o Compound Reaction Enzyme Gene o Compound Reaction o Compound Gene o Compound Note When selecting Compound as the Network Type a dropdown menu appears under Query providing the option of choosing between compounds or genes When any other Network Type is selected the only option is to use compounds genes unless using a selected pathway e Add or Remove data e Select a pathway o Use to view all the compounds and reactions associated with a metabolic pathway Select a specific pathway from the drop down list Saturated fatty acids beta oxidation Selenoamino acid metabolism Squalene and cholesterol biosynthesis T
11. e Gene gt Query Use compounds genes F Use selected pathway TCA cyde Output as File Node Attribute Browser Edge Attribute Browser Network Att Welcome to Cytoscape 27 3 1 Right click drag to ZOOM Middleclick drag to PAN Page 6 of 35 5 Click OK 6 If you enter a compound name it will map to its KEGG id a popup window will appear If there is more than one potential match use the dropdown arrow to choose the best match If the compound is not found in the system it will say Not Found One or more of fle compounds in your query had muliinle matches in the datahase Please select the mato ihat is best or none if you do not wish the compound fo aopear in ihe resite Input Name Potential Matches DL Lipo yl Ltysine DL Lipoyl Ltysine Glucose m CO0293 Mot Found 7 Click OK 8 After the experimental data has been loaded if any of the genes compounds that you submitted were not mapped to the database objects a Missing Data window will appear After viewing the Missing Data information click SAVE to save the data for later viewing or click OK to close the window without making it available for future viewing See the Missing Data Window section below under Option2 Load an experiment file for more information about missing data Page 7 of 35 Why are these elements missing The following input data could not be found in the MetScape database Compounds Trimethylamine
12. e display all compounds while the networks built from the list of Input genes compounds show only main compounds see Ma et al Mol Syst Biol 2007 3 135 for details Pathway Specific networks show all compounds Below is a table of available attributes for each edge es nn Attribute a Description fa Enzyme names Enzyme name jEnzyme ecnums Enzyme Comission number Reaction equation Equation for reaction Reaction locations Reaction subcellular location EHMN database Reaction pathway Pathway involving reaction Reaction reversible T reaction is reversible F reaction is non reversible Reaction rid Unique identifier for reaction canonicalName Common name interaction Type of interaction A 5 Select compounds and or edges in the graph to view their attributes in the Data Panel Page 18 of 35 Compound formula id id He e oF Ee Leukotriene D4 C25H40N2065 C glycolithocholate C26H42N04 _3alpha Hydroxy Sbeta t monn C24H4003 Am a ial PECES bi sa E hE hl a kn 4 lt a a pg een od a Compound pubchemcid Ci Eee e ee Pl i eet ines bist 5280749 H me m mam we Hi Notes e Some attributes such as Formula Mass and Smile apply only to compound nodes while others such as Enzyme Pathway and Reversibility apply only to reaction nodes e Other plugins used earlie
13. e two vertical squares with check marks will select all attributes Page 17 of 35 Below is a table of available attributes for each node type A B Attribute Description ID Compound approximateMWw Compound casnum Compound cid Compound file_name Compound formula Compound mw Compound name Compound pubchemcid Enzyme ecnum Enzyme name Gene filename Gene column_name Gene description Gene human geneid Genesymbol Gene geneid Reaction equation Reaction locations Reaction pathway Reaction reversible Reaction rid Type canonicalName Genelocations Unique identifier required by Cytoscape Compound Molecular weight integer data source EHMN database Chemical Abtracts Service compound identifier KEGG compound unique identifier Rows with data specific to your experiments Molecular formula Molecular weight Compound name PubChem compound identifier Enzyme Comission number Enzyme name Relative gene data values Gene data p value Gene description Human gene identifier Official gene symbol Ortholog gene ID if the input organism is not human Equation for a reaction Reaction subcellular location EHMN database Pathway involving reaction T reaction is reversible F reaction is non reversible Reaction identifier Node type gene enzyme reaction or compound Node name that is shown on node label Subcellular location Please note that the reactions shown in the Reaction equation attribut
14. ee 3 Anew window pops up titled Initialize Coupled Animation of Multiple Data Columns 4 Column headings from your data are listed on the right side of the new window Determine how many animations number of rows and data items per animation number of columns you will need Enter this information into the Rows and Cols boxes If you change these numbers from the default click on Reconfigure Layout Treatmenti_to Treatmenti_ti Treatmenti_t2 Treatment2_t0 Treatment2_t1 Treatment2_t2 5 Click and drag the column names into the grid to build the animation Page 26 of 35 8286 Sie Initialize Coupled Animation of Multiple Data Columns 5 b Mm Initialize Coupled Animation of Multiple Data Columns Network tite Subnetwork 1 Drag and drop labels from the iist on the left into the table of data labels for each animation Set the number of animations number of rows and the number of data items per animation number of columns in the text fields and Drag and drop labels from the list on the left into the table of data labels for each animation Set the number of animations number of rows and the number of data items per animation number of columns in the text fields and sconfigure Layout Rows 3 Cols 3 Reconfigure Layout Build Animation j to bnie t2 DataSeries_1 Control t1 iveatmenti t1 EMERE Dataseries 2 Control t2 f
15. grams The file format is identical to the input concept file Page 23 of 35 Citrate cyde TCA cyde 25 Cytokne cytokine receptor interaction DNA replication ematopoietic cell lineage Concept Selection METSCAPE RESULTS PANEL ADDITI ONAL NODE INFORMATION Additional information can be obtained for each node by double clicking on it To get additional information about any compound gene reaction or enzyme 1 Double click on the node of interest 2 On the right side of the screen the MetScape Results Panel will show up F 3 Use the scroll bar or click on the undock icon to see all the data Page 24 of 35 Compound Reaction Enzyme Gene weve Gene Node Entrez Gene ID Human glutamate decarboxylase 2 pancreatic islets and brain 65kDa Subcellular location s Golgi apparatus synaptic vesicle membrane perinuclear region of cytoplasm axon cytoplasmic membrane bounded vesicle v ANI MATI ON OF DATA Create an animation of the data to see how it changes over time and across treatments Building an Animation 1 Create a subnetwork for example create a subnetwork for the TCA Cycle See the Concept Selection Data in the Data Panel section for how to do this Note Itis not necessary to create a subnetwork before doing data animation the animation can be done on any network For example the Compounds file can have additional data columns see image below that
16. ilter tab 5 Click the Create Subnetwork button at the top of the Data Panel make sure you are on the Concept Filter tab 6 A new graph appears in the graph window This is the subnetwork for the selected concept Page 22 of 35 Control Panel sae COMpOUNd Reaction Enzyn Compound Reaction EnS62 751 Compound Reaction En 261 0 35400 a ia Ha 3 l 4 w i ks w f Ty oh i f te a N k r z Y E Me i me Th j a ii j Si M kA Hp Hr ory a l 7 1 i M i l i j I ahs ry hy 1 Ty i jt hay 1 ri s 1 7 1 Table Panel aa Wy Select All Concepts Tees z Concept Name IR FF 1 4Dichorobenzene deoradation ye 1 and 2 Meth 3 Chloroacrylic Acute myeloid Adherens junc x Se Alanine and asg tye Node Table edge Tabie Network Table Pat to 0 467 0 675 _ t 0 042 0 198 ag 62 The Reapply Selection button will re select the last selected concept in the graph If you select a concept and then select off of it clicking the Reapply Selection button will re select that concept The concept information can be saved as a file To save this information 1 Under Concept Filter tab click the Save Concepts button 2 Anew window pops up asking where to save the file Choose the desired location 3 Click Save The file saves as a CSV file that can be opened with most text editing or spreadsheet pro
17. is tool such as LRpath or GSEA from gene expression data Note Gene set enrichment testing is an approach used to test for predefined biologically relevant gene sets that contain more significant genes from an experimental dataset than expected by chance e GSEA Subramanian at al Proc Natl Acad Sci USA 2005 102 15545 15550 e LRpath Sartor et al Bioinformatics 2009 25 2 211 7 Below is a portion of an example concept file A B c D E F G H I 1 Concept name Concept type n genes coett odds ratio evalue Direction sig genes 2 Citrate cycle TCA E EEE 24399 24401 25179 25721 3 Fatty acid metab 05 up 24158 25363 25618 25757 140547 4 Alanine and asp a eo a up 24379 24401 25721 81670 81829 5 Reductive carbo 24368 24399 24401 25721 79250 6 Oxidative phosp KEGG Pathway 44 0 27758123 5 61284966 3 64E 05 9 89E 04 up 116550 291103 295923 301011 311 7 Urea cycle and up 24368 24379 24399 24401 24600 8 PPARsignalingp KEGG Pathway 32 0 28585824 5 90912002 _2 33E 04 0 00441518 up _ _ 24158 24450 25045 25757 29171 9 Carbon fixation up 24401 25721 81670 81829 114508 10 11 12 13 14 16 17 1 19 Arginine and pro KEGG Pathway 20 0 33385131 7 96259603 _5 14E 04 0 00699086 up _ 24368 24379 24399 24401 24600 Butanoate metal KEGG Pathway 30 0 263011241 5 12695967 0 00101503 0 01254945 up 24379 24399 24401 24450 25721 Valine leucine a K
18. isease gt Find MeSH Terms 2 Choose the appropriate identifier type and attribute Click OK 3 A hierarchical tree of MeSH Disease terms should be displayed in the Table Panel 4 Selecting a tree node will select respective metabolites in the network The numbers shown after the descriptors represent the number of matching metabolites in the active network Note Descriptors that have no nodes in the active network can be collapsed and hidden 5 To view relevant PubMed citations right click on a selected compound node and select MetDisease gt PubMed Citations For more information about MetDisease go to http metdisease ncibi org The MetDisease user manual can be downloaded at http metdisease ncibi org pdf MetDisease User Manual pdf Page 35 of 35
19. nded branches select Restore Original Network Creating a subnetwork A subnetwork of a current network can be created and will appear in a separate window A subnetwork will include all highlighted nodes and edges selected nodes should be yellow and selected edges should be red For example 1 2 3 Select the compound IMP Go to the Select menu in Cytoscape Choose Nodes gt First Neighbors of Selected Nodes gt Undirected Now all the first neighbors of IMP should be yellow Go to the Select menu in Cytoscape Choose Edges gt Select Adjacent Edges Now all the adjacent edges should be red Right click on IMP A menu of options will pop up Page 32 of 35 Edit Group Nested Networks adie MetDisease Rr MetScape 1 Create Subnetwork External Links Expand r Preferences Collapse ANJO N Restore Original Network 7 Choose MetScape gt Create Subnetwork Note When choosing options from the menu be careful not to move the cursor outside the menu panels Doing so will remove the highlighting of the nodes and edges resulting in an empty subnetwork 8 A new subnetwork is created in the graph window Page 33 of 35 Destroying a network To destroy a network no longer needed 1 Make sure you really do want to destroy the network e Cytoscape will ask you to confirm the deletion e Destroying the network is irreversible e Note If you want to destroy a netw
20. nel cc cc ccecccccesseccceseceeeeeececeeeecceeeeseceeeenecesseeceeeeneeeeeas 19 Pathway filter in the data panel ccccccecccccsssecccceseccccescceeeusececeeeceeceueceeeeuecessuaeceseeeceesenaeeetas 20 Concept filter in the Gata Dane cscciscsscnccseesacenscevecsicncdceacsainnesrencodensendvedeneneisuandiecatimeatenda ucboeiemades 21 METSCAPE RESULTS PANEL ADDITIONAL NODE INFORMATION cccccccsssssssssssssseeeeeeeeeeeeeeees 24 ANIMATION OF DATA ssssssseseeececcccceccceesaaauassssssseeeeececeeceeeeessssaauauasssseeeececeeeeeeeessssaaaaaaaasaaseeeeess 25 Building an APNE AU ON sic aces c dtc stetics epee west saeco ce coon testes seeeteea en oiesetes aeesatacasenaes 25 Manipulating the animation ZOOMING ccccccccsssccccesscccceesececcesecccceuscceeeusecessuneceseeeceeteneeeeeas 28 Manipulating the animation bar Chart ccccccccsscccccsseccceesececeeseceeceecceeeuseceseunecesseeceeseeeeeenas 28 Playing the animation pos saeco stares ntcnce seaacunessnenasocnnsdeacuaracusaabnedsaaeinasaiannasd ARTERE apai 29 MANIPULATING NETWORKS 000 cccccccccccsssssssssssseeeccccccececcessssaaeasssssseeeeeeceeeeeeesessssauaaaaesssseseeeeeeeeeeeeess 29 Expanding a IU OU oec E E OEA 29 Option 1 Expanding a network in the current network window Example using Compound Reaction Network sete irc sa te sects eta pans neato hse eanpeeontnsaeasecasatuencaoaecndeineresu
21. ork view without destroying the network itself use Destroy View instead of Destroy Network 2 On the Network tab in the Cytoscape Control Panel right click on the network you want to destroy and select Destroy Network Note If you destroy a network that has subnetworks the subnetworks are NOT destroyed They are promoted up one network level SAVING AND REOPENING A SESSION Saving a session To save a Cytoscape session containing one or more MetScape app networks 1 2 3 4 Select File gt Save or Save As from the Cytoscape menu Browse to a location for saving the file Name the file Click Save Reopening a session To reopen a saved session containing MetScape app data 1 2 Select File gt Open from the Cytoscape menu Navigate to the saved file location Select the file Click Open After Cytoscape reports that the session file was successfully loaded click Close Page 34 of 35 SUPPLEMENT METDISEASE APP MetDisease is designed to annotate metabolites with Medical Subject Headings MeSH disease terms The underlying data comes from the Metab2MeSH data set Sartor et al Bioinformatics 2012 May 15 28 10 1408 10 To use MetDisease you need a network of compounds with KEGG or PubChem Ids or compound name If using MetScape 2 3 2 or higher you can use MetDisease on the MetScape networks How to use MetDisease Once you have built a MetScape network 1 Select Apps gt MetD
22. ose C R E G couplings that match both a compound from the compound input and a gene from the gene input are used Page 15 of 35 If a concept file is provided genes from that file will be used as input instead of the genes from a provided gene file If only a gene file is provided all genes from that file are used as input In this case we recommend that you load a smaller set of genes e g most significant differentially expressed genes e Compound C networks built from compound input If a list of compounds Is provided the resulting network will include the query compounds shown in red plus any compounds that participate in the same reactions as query compounds The edges will be drawn between seed compounds and their neighboring compounds e Compound C networks built from gene input If a list of genes is provided the resulting network will include the compounds that are related to the query genes via the reactions in which they participate and the enzymes that catalyze these reactions The edges will be drawn between all compounds e Pathway networks Pathway specific C R E G C R and C G networks are built from a set of genes enzymes reactions and compounds defined in the EHMN database Pathway specific Compound networks are built similarly to the Compound networks built from a set of input genes DATA PANEL DISPLAY Attributes of compounds reactions pathways and concepts that you have selected in the ne
23. r in your Cytoscape session may leave behind attributes that don t apply to MetScape compound or reaction data Rearranging attributes in the table panel To reorder attributes in the Table Panel click on an attribute column heading and drag it to a new location Page 19 of 35 Compound pubchem 5280749 C05952 Leukotriene E4 N 6435286 C05951 Leukotriene D4 _ glycolithocholate_ ee 5280749 05952 6435286 C05951 eee N Node Table Edge Table Network Table Pathway Filter To sort by an attribute click the attribute column heading to sort in the reverse direction click again Compound pubchemcid 3 amp Compound name Compound cid 5280749 Leukotriene E4 oe Leukotriene D4 aan glycolithocholate roxy 5beta cholan E i b oe es Lr Arar a Pathway filter in the data panel MetScape provides two ways to access pathway information The Pathway Filter tab lists all pathways represented in the network Selecting one or more pathways will highlight in the network all nodes in the pathway s Pathways are also displayed as attributes in the data panel Page 20 of 35 Table Panel ay x 1 Select Al Pathways Deselect AlPathmays J Create subnetwork nnl Pathways Joxo i0R octadecatienoate beta oxidation Amingsugars metabolism oe Androgen and estrogen biosynthesis and metabolism
24. ret metabolomics and gene expression data in the context of human metabolic networks MetScape uses a metabolite database developed by extracting and integrating information from the following sources 1 Edinburgh Human Metabolic Network EHMN http www ehmn bioinformatics ed ac uk 2 KEGG COMPOUND Database http www genome p kegg compound MetScape allows users to load a list of metabolites with experimentally determined concentrations a list of genes with experimentally determined expression values and a list of concepts or pathways and display them in the context of relevant metabolic networks Workflow overview With MetScape you can Trace the connections between metabolites and genes Integrate multidimensional data Visualize compound reaction enzyme and gene networks and display compound structures as well as information for reactions enzymes genes and pathways Visually animate changes in compound concentrations over time and across experimental conditions The basic steps in the workflow include i Enter data You can type or paste a list of compounds and or genes load a file containing experimental data or start from a biological pathway Select compound and reaction attributes Choose which attributes to display ina table as you work with your visual network graph Explore the visual network and table of attributes e Expand and collapse a network e Create a subnetwork e Visualize
25. rihydroxycoprostanoyl CoA beta oxidation Tryptophan metabolism Tyrosine metabolism Urea cyde and metabolism of arginine proline glutamate a e Save the Output as a File e Build Network graph based on the data Page 14 of 35 Control Panel Fa work VizMapper Editor Filters p gt N pre Input Organism Human Experimental Data Compounds human _metabolites4metscape _ NAMES Genes none Concepts none Compounds Options Network Type Compound Reaction Enzyme Gene Query Use compounds genes 0 Use selected pathway TCA cyde Bul Network Note When the organism is human the Genes section will show Input ID and Input Symbol However when the organism is not human ex rat the Genes section will show Input ID Input Symbol and Human Symbol RULES USED TO BUILD DIFFERENT NETWORK TYPES e Compound Reaction Enzyme Gene C R E G Compound Reaction C R and Compound Gene C G networks The C R E G C R and C G networks are all built from the same underlying data That data Is derived in each case by finding compounds that participate in reactions that are catalyzed by enzymes that are encoded by genes If only genes are input then all the enzymes reactions and compounds that match those genes are used If only compounds are input then all the reactions enzymes and genes that match those compounds are used If both genes and compounds are Input then only th
26. rreatmenti t2 Unden RO 6 After grid is completely filled in click on Build Animation Note If you want to undo what you filled out in the grid click on Restart and the grid will be cleared 7 Three new windows appear in the graph panel each representing a different treatment In addition an Animation Controls window appears e l DataSeries 21 EEE i ija g F shed l p is bs F fab a waite gt weir vice i E sae j 2 B A ae a i f E 5 nm ha iu ih Page 27 of 35 Manipulating the animation zooming 1 Zoom in on one graph to the appropriate view size zoom the same way you do with any Cytoscape graph 2 On the Animation Controls window click on Realign All This brings all the treatment graphs to the same view Lj DataSeries_01 CoA 2 ate o E 2 DataSeries 11 CoA 2 ate 4213 3420 A Manipulating the animation bar chart 1 The bar chart in the Animation Controls window shows the range of the data and its frequency The range of measurements are on the x axis while the frequency with which they occur in the experimental data set are on the y axis 2 Click on a bar in the bar chart and a vertical line slider will show up on the bar chart The slider can be moved by clicking on the bar chart and dragging the line When moved the values shown in black are also shown in black in
27. significance values and fold change values A B C 1 Fold Change P value 2 COO0D02 0 51 0 0061 74265 3 cooo 1 14 0 646801 75 4 CO0008 0 99 0 970303452 2 C00020 2 12 0 06805286 5 6 COO025 0 91 0 115376267 7 000037 0 99 0 90465s012 amp COO041 0 95 0 574835153 9 COO04 1 09 0 809172269 10 cooo 0 56 O 100 24407 11 cooo 136 0 189989302 12 C0000049 0 92 0 755789133 13 C0006064 0 45 0 166 07162 14 CO0065 1 22 0 8051510 8 15 c00073 0 80 0 356405 722 Gene File The gene file must meet the following requirements e The first row must be a heading row that includes column headings to label the data e The first column contains Entrez Gene IDs or Official Gene Symbols e The remaining columns contain experimental data Multiple experimental values are permissible in the same spreadsheet Page 9 of 35 Below is a portion of an example gene file with Gene IDs significance values and fold change values A B C 1 ENTREZ GENE ID Pvalue Log fold change 2 1 0 002335904 0 02 3 2 2 07E 08 0 06 4 2 2 03E 08 0 04 3 9 0 003919472 0 04 5 10 0 00026716 0 08 T 12 0 000237925 0 05 B 13 0 002469364 0 053 g 14 0 506396205 0 00 15 8 25E 06 0 04 16 0 022222108 0 01 18 1 47E 08 0 07 18 5 24E 06 0 09 18 2 12E 05 0 07 15 19 0 820594937 0 00 16 19 1 76E 08 0 06 17 19 9 46E 09 0 04 18 19 0 660631201 0 00 19 20 1 16E 07 0 05 Concept File The concept file can be generated by a gene set enrichment analys
28. st The below warning window will pop up in this situation Missing Data Window After the experimental data has been loaded if any of the genes compounds that you Submitted were not mapped to the database objects a Missing Data window will appear Genes compounds and concepts may appear on this missing elements list because e Genes and compounds that you supply may not be in the database If they are not found in the database then they are reported as missing Page 12 of 35 e If your input genes are not human Rat for example then they are mapped to human genes using homologs from NCBI s HomoloGene If this mapping fails then those genes are reported as missing e MetScape will display only the genes that encode metabolic enzymes If an input gene does not encode metabolic enzymes it will appear on the missing elements list e A concept pathway will appear on the missing list if all of its significant genes are missing The list of significant genes for a concept comes from the input file or from LRpath After viewing the Missing Data information click SAVE to save the data for later viewing or click OK to close the window without making it available for future viewing Missing Data VI SUALI ZATION Access the MetScape Legend from Apps gt MetScape gt Show Legend Fm Legend Compound Reaction Enzyme Gene Input Significant Expansion gt Close Page 13 of 35 Additional inform
29. t Example of selecting experimental data including importing files and designating fold change p values and thresholds Select Experimental Data 52 Data hoose species Organism Human Compounds Select experimental data ore P value none Fold Change none 4 Genes Select experimental data one P value none Fold Change none Concepts Select experimental data none Generate a concept file from genes using LRPath Example of ID mapping window from a loaded compound experiment file Page 11 of 35 Select names for compounds One or more of dhe compounds in your query had multiple matohes in the database Please select the maich thats best or none if you do not wish the rs Input Name Potential Matches KEGG ID Protein glutamine Protein L glutamine Protein M5 alkylglutamine ala val TO ig 00123 L r ma O S ma e aea enn mesa O S ee Note If you select Save on the Select Compound Mappings window you will get a csv file containing mapping information for all compounds that MetScape successfully mapped Note The Select Experimental Data window can also be accessed from the MetScape tab Note Multiple networks can be built within the same user session After a network is built pull up the Select Experimental Data window and change the data files Then build the new network Both networks will remain accessible If you change species however all existing data will be lo
30. the graph and the set of the color scale is reset 3 The selected portion of the graph determines what the animation will show This allows outliers to be removed if desired 4 The color range can be changed by clicking the dropdown arrow next to Red Blue Page 28 of 35 Select Color Range Eren Red Blue Playing the animation To play the animation click Play on the Animation Controls window Colors and node sizes change within the three treatments showing changes over time To stop the animation click Stop on the Animation Controls window 1to the network view ynto the source node then click on id edges specified in SIF format to create a node yin an edge and specify the source on the target node to finish the JDaaPaed a UU GS Animation Controls Subnetwork 1 Column 0 Column 1 Column 2 a ser Concept Selection MANIPULATING NETWORKS Expanding a network From a compound node you can expand the current network to include additional reactions and related compounds genes and enzymes Option 1 Expanding a network in the current network window Example using Compound Reaction Network Page 29 of 35 1 Right click on the compound node you want to expand this node is known as the expansion seed node A menu of options will pop up 2 Goto MetScape gt Expand gt Expand in Existing Network Create Supgfetwork
31. twork appear in the Cytoscape Table Panel Choosing attributes provided through MetScape To choose which attributes to view 1 To choose attributes for compounds click the Node Table tab in the Table Panel You can choose to view node edge or network attributes by clicking on the respective tabs at the bottom of the Table Panel Pathway data can be viewed under the Pathway Filter tab and concept data can be viewed under the Concept Filter tab in the Table Panel 2 Click the Show Column icon in the Table Panel toolbar A list of attributes with check boxes will appear Page 16 of 35 ES 2s a Bu ae a F lt EE f Compound Reaction Enzyme Gene caepoy snared Genea Readio Reaio Genes reacio ci AA l oo m Node Table Pathway Filter 3 Un select the attributes you do not want displayed in the Table Panel Attributes are listed with item type before the attribute ex Compound name Enzyme name The available attributes will depend on the type of network created Table Panel A F Y 0 IE i fr Camnons Compound formula share E Compound mw Compound name Compound pubchemcid F Compound smiles Enzyme ecnum Enzyme name V Gene description l 4 When you are done click anywhere outside of the list and the table will be populated with the appropriate data Note In Cytoscape 3 0 the two empty vertical squares will un select all attributes Clicking th
32. your data in a wide variety of network layouts provided by Cytoscape e Use color size and other effects to visually reflect a set of attribute values Save your session and reopen it later Page 4 of 35 Installing Cytoscape and the MetScape app on your local computer 1 Install Cytoscape on your computer For more information go to the Cytoscape website at http cytoscape org 2 After Cytoscape is installed start the application 3 To install the MetScape plugin select Apps gt App Manager from the Cytoscape menu 4 Under the Install Apps tab scroll down until you find MetScape in the second column amp Download Site http apps cytoscape org Search all apps 44 dns Ea MetScape apps by tag GeneMANIA 3 0 2 installed 3 0 1 jActiveModules JEPETTO KEGGscape Maps human mouse and rat KeyPathwayMiner metabolomics and gene expression data MCODE Installed to human metabolic networks and MetDisease enables pathway analysis l oMetScape Tr 3lled FathExporeNy Pathway Scoring Applicat PEPPER PINASMS Venn and Euler Diagrams 5 Click on the MetScape app 6 Click Install 7 When installation is complete click Close A MetScape option is added to the Cytoscape Apps menu Registration MetScape is a free program We ask you to register because it helps us to
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