12、國(guó)外研究所收集谷歌cytoscape相關(guān)-google

1、Discussion summaryCytoscape introductionThomas Skt JensenCenter for Biological Sequence AnalysisThe Technical University of DenmarkSub-cellular localization coverageCo-localization of interacting proteinsTendency to interact with your cousinOver-representation of highly abundant proteinsCoverage ver

2、sus Accuracysay a lot, of which most is wrongsay a lot, of which most is rightsay little, of which most is wrongsay little, of which most is rightSpecificitySensitivityVisualizing protein/gene relationships A short introduction to CytoscapeOutlineVisualizationWhy Cytoscape?Getting startedAttributes

3、for nodes and edgesExamplesVisualizationSystems Biology - looking at a systema collection of units (gene/proteins) in a contextMassive amounts of protein/gene relationshipsa lot of undiscovered biology is hiding in that dataimpossible to get an overview if investigated by handIntegrate many types of

4、 relationshipsthe data is available in the CBS data warehouseWhy Cytoscape?Cytoscape ( )can visualize relationshipsis easy to usehas an advanced color coding schemeallows for custom made plug-inshas a strong communityis free for academiaGetting startedTwo types of input formatsGML: a graphical marku

5、p languageSIF: a simple input formatNodes (genes/proteins) and relationships are specified in one fileGML - nodeGML example:nodeid37label37graphicsx411.0y395.0h34.0w122.0fill#ccccfftyperectangleGML - edgeGML example:edgesource210target92labelPPographicswidth1.0typelinefill#000000SIFVery simplenode_1

6、 edge_label node_2node_3 edge_label node_2node_4 edge_label node_2node_5 edge_label node_6node_7 edge_label node_1SIFYDL224C pp YER059WYDL224C pp YIL050WYDL224C pp YML064CYDL224C pp YNL189WYDR386W pp YBR009CYDR386W pp YBR098WYDR386W pp YCL032WYDR386W pp YDL043CYDR386W pp YDL208WYDR386W pp YDR363WYDR

7、386W pp YDR381WYDR386W pp YER006WSIF Example : protein-protein interactions in yeastNode and edge attributesColoring based on attributesNodes; cell cycle regulated, tissue type, etc.Edges; ppi, protein-DNA, etc.Expression dataNode_idexp1 exp2 exp3 exp4.Node annotation partmentYAL001C = transcription

8、 factor TFIIIC complexYAL002W = membrane fractionYAL003W = ribosomeYAL005C = cytoplasm*YAL007C = COPII-coated vesicleYAL008W = mitochondrionYAL009W = integral to membrane*YAL010C = mitochondrial outer membraneYAL011W = nucleusNode annotationCellCycleRegulatedYAL001C = 1YAL007C = 1YAL012W = 1YAL021C

9、= 1YAL022C = 1YAL023C = 1YAL024C = 1YAL034W-A = 1YAL039C = 1YAL040C = 1YAL053W = 1YAL067C = 1Edge annotationProtein-DNA binding dataMBF pd YER059WMBF pd YIL050WMBF pd YML064CYML064C pd YNL189WYML064C pd YER059WYML064C pd YBR098WYBR098W pd YCL032WYBR098W pd YDL043CYDL043C pd YDL208WYDL043C pd YDR363WYDL208W pd YDR381WYDL208W pd YML064CEdge annotation:ActivationRepressionMBF (pd) YER059W = 1MBF (pd) YIL050W = 0MBF (pd) YML064C = 1YML064C (pd) YNL189W = 0YML064C (pd) YER059W = 0YML064C (pd) YBR