Home

Help

1. gt Node Visual Mapping i Edge Visual Mapping A 2 Import network You can click File gt Import gt Network From Multiple File to import network with the format XGMML GraphML and SIF Otherwise you can click File gt Import gt Network From Text File to import network from text file separated by specific delimiter Nok import network from text file Ee Interaction Definition asoan Source Interaction Interaction Type Target Interaction Columns in BLUE will be loaded as EDGE ATTRIBUTES Advanced o Weawdakygoer kiksa C Show Text File Import Operation gt Node Visual Mapping Preview gt Edge Visual Mapping Left Click Enable Diable Column Right Click Edit Column import Cancel a After importing network the layer above region A and B will be removed and you will see figure Region A is used to show the numbers of node and edge in the current network Region B is the visual style container with which user can define more than one visual styles Region C shows the global visual style Region D contains the panels of visual mapper and filter Region E is the main menu with which you can import network export network import attribute of edge and node and layout network Region F is the screen to show the network Region G is the panel for setting attribute of node and edge in network Region H
2. You must select at least one from Gene Gene Interaction Chromosome Position Interaction Transcriptional Factor Target Gene Interaction Kinase Target Gene Interaction and String Protein Interaction Gene Gene Interaction is defined as the interaction abnormal function for two genes of which at the same time can result in a aberrant phenotype Chromosome Position Interaction is defined as the interaction two genes of which locate at the same chromosome region In the String Protein Interaction the main difference between String Protein_Actions and String Protein_Links database is that String Protein_Links contains known and predicted interactions and String_Protein_Actions only contains known interactions The parameter filter indicates the cutoff for the strength of interaction The bigger value of filer can result in more reliable interaction and by contrast it can result in interactions of higher coverage Input Gene List Cl Gene Gene Interaction Database BioGrid Primary Interaction L chromosome Position Interaction Database Secondary Interaction MI GSEA C Transcriptional Factor Target Gene Interaction Network Filter Database TFTG_Set1 Kinase Target Gene Interaction Network Regulation Database PhosphoPlus Network Node Annotation CI String Protein Interaction Database String_Protein_Actions O
3. is used to show the attribute of node or edge when you select nodes or edges in the network File v Style v Layout Nodes 24 Edges 34 urrent Visual Style cytoscape VisualMapper Filter gt Node Visual Mapping gt Edge Visual Mapping D 3 Import attribute You can click File gt Import gt Attribute From Multiple File to import attribute of edge or node from text file separated by specific delimiter In the panel the Attributes indicates whether importing node attribute or edge attribute The Attribute Type indicates the store type of attribute value in the network The first line of attribute file is attribute name other lines follows the format like id delimiter value The id is node id or edge id of the network and the value is the corresponding attribute value The sign delimiter represents the delimiter used in your file The detailed format of attribute file is the following Attribute name idi delimiter value id2 delimiter value import attribute from text file Data Sources 5 3 Attributes Node O Edge Attribute Type string O integer number boolean Delimiter Equal sign OTab Ocomma O Semicolon Ospace O Other ViawdMiamme kiss gt Node visual Mapping Edge Visual Mapping InputFile Select File 4 Network layout Click Layout and you will see Recalculate layout Layout Styles Preset Layout and Set
4. the same cellular event such as biochemical interaction catalysis protein binding protein modification and so on Protein Complex Interactions is defined as the interaction two genes of which belong to the same complex At least one is checked for parameter Database of every type of interaction The parameter Expansion Level means that whether you only find interactions among seed gene or add new genes interacting with previous adjacent layer The new genes can be layer first second and third The parameter Interaction In Level means that whether to find interactions among genes in the same layer when you expand network to specific layer Input Gene List Cl Pathway Interaction Database Primary Interaction O wikiPathway Reactome o Reactome_FI_Curated F Reactome_FI_Predicted Secondary Interaction Fj PathwayCommons Fl KEGG O nci CO EHMN Network Filter Expansion Level seed O First AEE AA EE Interaction In Level No O yes Network Node Annotation m C Protein Complex Interaction Database MIPS CORUM Download Network File Expansion Level Seed O First M Mi Protein Protein Interaction Database HPRD O BioGrid O DIP O mint O Intact O BIND Expansion Level Seed first Second O Third Interaction In Level No O yes e Reset Submit Step 3 Select the parameters of Secondary Interaction and submit to iBIG
5. Downstream Upstream J Downstream Network Node Annotation Download or Visualization Step 6 Select the parameters of Network Node Annotation and submit to iBIG This step is composed of gene annotation sets You can select specific sets to annotate genes in the built network Input Gene List Pathway Annotation Database Reactome wWikiPathway KEGG Primary Interaction O NCI EHMN PathwayCommons O Protein Complex Annotation Secondary Interaction Database MIPS CORUM Network Filter CI chromosome Position Set Annotation Database GSEA Network Regulation F Transcription Factor Annotation Database TFTG_Set1 Database Name Tarbase I miRecords C MicroCosm Database Status validated Predicted Download or Visualization Cl kinase Annotation Database PhosphoPlus Fj Epigenetics Gene Annotation Database ncBI Go O Housekeeping Gene Annotation Database HK_Set1 O Tissue Specific Gene Annotation Database GsE16546 C MicroRNA Annotation F 1 GO_BP Gene Annotation n Step 7 In this step the built network has been stored on the iBIG you can choose to download the network in the format of xgmml or to visualize it You must input the network name in the parameter Network Label and select the type of gene id in the output of the built network Inp
6. Set Annotation chr_position m Transcriptional Factor Annotation MicroRNA Annotation microRNA Kinase Annotation kinase Epigenetics Gene Annotation epigenetics Housekeeping Gene Annotation HKG Tissue Specific Gene Annotation TSG GO_BP Gene Annotation GO_BP GO_MF Gene Annotation GO_MF GO_CC Gene Annotation GO CC
7. String_Protein_Links Filter 150 O 300 O 450 O 600 O750 900 Download or Visualization a Submit Step 4 Select the parameters of Network Filter and submit to iBIG When you have expand network to layer first there are additional genes which are not only belonging to seed genes but also considered as bridge node to make seed genes indirectly interact The parameter bridge node can only keep left genes considered as bridge nodes and filter out other genes in layer first Input Gene List Cl Bridge Node i bridge_node yes Primary Interaction Secondary Interaction Network Regulation Network Node Annotation Download or Visualization Step 5 Select the parameters of Network Regulation and submit to iBIG After you have gone by Input Gene List Primary Interaction Secondary Interaction or Network Filter the network on you purpose has been built In this step you can find upstream regulators and downstream targets of the network Input Gene List C Transcriptional Regulation Database TFTG_Set1 Primary Interaction Upstream or Downstream V Upstream C Downstream CI MicroRNA Regulation Database Name Tarbase J miRecords C Microcosm Database Status validated O Predicted Secondary Interaction Network Filter LC kinase Regulation Database PhosphoPlus Upstream or
8. User s Manual 1 Building network iBIG is web tool for building and visualizing network It is a knowledge based tool which integrated much information for gene interactions and annotations from various public data You can follow the following step to build network based on the gene list submitted by you Notice the valid results of every step will be added into the cached network If you want to rebuild network you must clear the cached network by resubmitting gene list in the Input Gene List step Step 1 In Input Gene List upload the seed genes with which you will build network The format of text area is one gene each line There are three types of gene id iBIG supports such as Entrez_GenelD Gene Offical Symbol and Gene Symbol Notice that Gene Symbol can be selected when you are not sure that the symbol of genes is the official gene symbol Input Gene List Primary Interaction Secondary Interaction Network Filter Network Regulation Gene Identifier Type Network Node Annotation O Entrez_GeneID Gene_Offical_Symbol Gene_Symbol Reset Submit Download Network File Step 2 Select the parameters of Primary Interaction and submit to iBIG You must select at least one from Pathway Interactions Protein Complex Interactions and Protein protein interactions Pathway interaction is defined as the interaction two genes of which participate in
9. ame of current filter In the region of filter definition Attribute indicates the attribute on which adding new filter condition will be based Clicking button Add can add a new filter condition If negation is checked the final logical for all of the added conditions will be reversed If the not in every condition is checked this condition will be reversed The logical AND and OR between any two conditions decides the logical for them Each of conditions can be removed by clicking button Network File Style v Layout v Nodes 24 Edges 34 Current Visual Style cyloscape v Gl ad DefaultFilter v Ge 5 Fiter Definition Attribute Attributes add Negation O Apply Filter 3 Abbreviation of attributes for node and edge The Node _ Level attribute for node indicates the layer gene reside at in network The UpDown attribute for node indicates the character in network regulation The meanings of other attributes is the followings PathiR PrCpxIR Pathway Interaction Protein Complex Interaction Protein Protein Interaction G G ChrPIR TFTG KinaseTG SP MicrornaTG TFTG KinaseTG Gene Gene Interaction Chromosome Position Interaction Transcriptional Factor Target Gene Interaction Kinase Target Gene Interaction String Protein Interaction MicroRNA Regulation Transcriptional Regulation Kinase Regualtion Pathway Annotation pathway Protein Complex Annotation complex Chromosome Position
10. n the data panel Click button E to add attribute into network Click button to delete attribute from network Click button to select which attributes to be exported 7 Visual style container Clicking button will show the panel to set visual style container Click create new visualstyle to create new visual style Click remove current visualstyle to remove current visual style Click rename current visualstyle to change the name of the current visualstyle When you change the current visual style the style of network will change at once 8 Setting global visual style of network Click the bar with word Default the Default Apperance panel will show In this panel you can set graphics of network like that in standalone cytoscape a C Newle lt 24 Kag A Cann Vi Q AD Ge 4 Default Apperance x EET I ia Apply 9 Visual mapper Click the tab VisualMapper in the region D to use the panel of visual mapper like that in standalone cytoscape The default value for variable of visual style and mapper type is none When a network is loaded you can select specific attribute for any variable of visual style and appropriate type of mapper to set visual style of network If you again set none for value of variable of visual style and mapper the visual style from this setting will be removed Network File v Style v Layout Nodes 24 Edges 34 Current Visual Style cytoscape a Defaul
11. tings in the submenu Clicking Recalculate layout layout of network will be recalculated Layout Styles includes four layout algorithms that can be directly applied to current network and Settings is used to adjust parameters of four layout algorithm Preset Layout provides the way to layout network with your information on preset node position Each line of preset layout file represents position of one node of the network The format of line is id delimiter x coordicate delimiter y coordinate The id is the node id of network The sign delimiter represents the delimiter used in your file The detailed format of preset layout file is the following Id1 delimiter x coordicate delimiter y coordinate Id2 delimiter x coordicate delimiter y coordinate Neale Belge E amp Dhedinniles r Import Node Coordinates m Data Sources Delimiter Equal sign Tab O comma O Semicolon OSpace O other InputFile Select File Meanie kee Node Visual Mapping gt Edge Visual Mapping impor M ansa acai tiiegs 5 Network style The menu item Style has three submenu items Merge edges Show node labels and Show edge labels Merge edges merges two edge between two nodes into one edge Show node labels decides whether to show node labels and Show edge labels decides whether to show edge labels 6 Setting network attribute Click button to select which attributes to be shown i
12. ts oe VisualMapper Y Node Visual Mapping gt Node Size None gt Node Color None gt Node Shape None gt Node Border Color None gt Node Font Face None gt Node Font Size None gt Node Label None gt Node Label Color None gt Nodel Label Width None gt Node Label Opaa None gt Node Label Positi None gt Node Line Width None Node Opacity None MW Sa M a a a ae EEE gt Node Toolnp None gt Edge Visual Mapping 10 Visual mapping bypass Select one node or edge in the network and rightclick on the selected element then click Visual Mapping Bypass you can reset visual style of the selected element gt Z Q amp http 192 168 21 90 isuaization start_visualization Os2 f gt i agge o0o 0e n amp Dr Network Nodes 24 Edges 34 Cusrent Visual Style cytoscape ye Defaults Delete sode Add new edge then click the target node Add new sede VisualMapper Filter Delete selected RE 2ER HF Adobe Flesh Player 10 3 131 28 Node Visual Mapping gt Edge Visual Mapping 11 Filter Click the tab VisualMapper in the region D to use the panel of filter like that in ma standalone cytoscape Click button to show the panel for setting filter container This panel are composed of create new filter used to create new filter remove current filter used to remove current filter and rename current filter used to change n
13. ut Gene List Now you can download the network you have just constructed in the xgmml format N Network Label Primary Interaction Gene Identifier Type Entrez_GeneID Gene_Symbol Download or Visualization Download Visualization Secondary Interaction Network Filter Network Regulation Network Node Annotation 2 Visualizing network Visualization part of iBIG is a web based tool for visualization network It is developed based on Cytoscape web API version 0 7 4 Just enjoy it with the thinking as same as standalone Cytoscape 1 Staring cytoscapeweb Click the Visualization in the red box visualization will start iBIG A tool for building and visualizing network Input Gene List Nov 15 BIG 1 0 i ae release Nov 15th A Welcome to iBIG a web based tool for building and visualizing interaction network of 2011 sie eee an gene and gene set Itis simple and easy to work with and it comes in some different i flavors Links To Secondary Interaction Cytoscape Web Cytoscape Network Filter Contact Any advices or comments are welcome Please Network Node Annotation contact us by sunjy big ac cn Network Regulation Download or Visualization 2010 BIG Design by Sun jiya After it is started you will see its interface similar to the standalone Cytoscape Because there is no network loaded the region A and B is covered by layer feoedebages ero

Help

Contents

Download Pdf Manuals

Related Search

Related Contents