![]() Step 1: remove duplicated edgesSometimes nodes are linked by more than one edgeMultiple evidence for interactionRemove them for clustering and simpler visualizationĪll clustersSorted by sizeSelect a clusterStep 3: look at the results I) Find and annotate dense areasUse an app that clusters the networkBiological assumptionWe look for protein communitiesMany interactions withinProbably share functionGene function prediction Node colorEach column represents some information that we have (this is a column in the node table data)Discrete: set a value for each type of informationApplicationsAppsCytoscape has many tools called AppsInstall by going to Apps -> App ManagerApplications supportAdvanced analysisBiological analysisIntegrating dataImport special data Open and modifyThe IntAct netowrk: node color Try to position the nodes so that there are as few crossing edges (and such that the edges are of more or less equal length if possible)Change layout scale Places all of the nodes in a circular arrangement.Very quick Partitionsthe network into disconnected parts and independently lays out those parts.Force-directed Sanity check: close Cytoscape and load the session!RemarksAt this point we know how to load data from databases and filesWe can perform simple navigation, zoom and saveWe saved different networks each had its own visualization rulesA good habit that saves troubles: save a session for each visualization typeMultiple networks, but keep a consistent visualizationModifying and saving a visualizationCytoscape supports many visualization optionsLayoutsNode size, color, labelEdge width, line typeTo save the graph as a high quality image: The sub-network was created below the original networkSave the sessionWe imported six networksBefore we start modifying them lets save the sessionFile -> Save Load data: OWLGood for looking at pathwaysThis example: data from the Reactome databaseįocus on a selected region (nodes in yellow)Zoom: result OPTIONAL: Click on the columns that you want to be kept as attributesResult Set where to look for the nodes and the typeLoad data: from a table Text: name1interaction_typename2Load data: from a tableFrom excel files or tab-delimited text tables The new network Load data: from filesWe sometimes have our own dataFrom papersA special search in a databaseOur experiment (e.g., correlation between genes)Famous formatsSIFA table OWL for pathways, complex textBut easy to get and very informative once uploadedLoad from filesĬontains an interaction network of 331 genes from Ideker et al. Information about the marked nodesLoad data: import all interactions Look at a networkThe toolbar, contains command buttons, the name is shown when the mouse pointer hovers over it.Main Network ViewControl Panel: lists the available networks by nameNetwork Overview Pane: move around!Table Panel: displays node, edge, and network table dataSearch for a gene The imported networks by nameBasic statistics The initial window enables searching in the big public databasesLoad data: import from databasesSearch example: by gene name The toolbar, contains command buttons, the name is shown when the mouse pointer hovers over it.Main Network View, initially blank.Control Panel: lists the available networks by nameNetwork Overview PaneTable Panel: can be used to display node, edge, and network table dataLoad data: import from databases OutlineBasicsLoad and visualize dataCustomizeApplicationsClusteringEnrichment analysisGeneMANIAIntegrative analysis: Modmap and DICERGene expression analysis (inclusing jActiveModules)Creating co-expression matricesCytoscape BasicsInitial window Gene co-expressionProtein-protein interactionGenetic interaction55CytoscapeCytoscape is an open source software for integrating, visualizing, and analyzing networks. 2011 Natureīiological interaction networksNodes: genes/proteins or other moleculesEdges based on evidence for interaction Cytoscape and networksDavid Amar overview (and disclaimers)Cytoscape is the most used tool for network analysisWe shall first cover the basicsOur goal is to get a (good) taste, and to see how easy it is to get and analyze dataWe will then move to advanced analysesCytoscape Apps and external toolsSlides cover >2 hours, take what we will not cover as exercisesThe slides show analysis in Cytoscape 3.1.1Network biologyOverview: systems biologyRepresent molecular entitiesRepresent interactionsTwo main data typesPathwaysInteraction networksīiological interaction networksNodes: genes or other moleculesEdges: evidence for some interaction can contain weights, directionsMagtanong et al.
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