Cytoscape Workshop at Salk 12/4/2012

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Presentation slides for Cytoscape Workshop at Salk 12/4/2012.

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Cytoscape Workshop at Salk 12/4/2012

  1. 1. CytoscapeAn Open Source Platform for BiologicalNetwork Analysis and Visualization Keiichiro Ono Cytoscape Core Developer Team University of California, San Diego Trey Ideker Lab 1
  2. 2. Thanks for Attending!- Who am I? - Keiichiro Ono - Cytoscape Core Developer since 2005 - Area of Interest: Data Integration & Visualization - University of California, San Diego Trey Ideker Lab 2
  3. 3. Outline- What is Cytoscape?- How to Use Basic Features of Cytoscape- Cytoscape 3 and Beyond 3
  4. 4. What is Cytoscape?
  5. 5. Cytoscape - Open source platform for biological network data integration, analysis, and visualization 5
  6. 6. 6
  7. 7. - Free! (LGPL)- Developed and maintained by universities, companies, and research institutions- De-facto standard software in biological network research community- Expandable by Apps
  8. 8. JUN FANCB GATA3 KRT14 HSPA8 FBXL3 DDB1 TSPAN17 CDC25A CDC45 CDKN1A PAX6 APLP2 EIF4G1 TOP3APEG3 CHEK2 TUBB2A POU2F1 HIC1 FLI1 CTCFL PML MAP3K4 NUP153 DCAF11 EZH2 RNF31 ERCC2 EGFR SMARCE1 AKAP10 NUSAP1 FANCA MED21 RAD9A CDKN1B HMMR WRN MRE11A ETS1 AP2B1 ESR1 UBE2I XRCC5 RBL1 TSPAN9 NMI RNF144B SHFM1 ERCC1 RNF8 SUGT1 WT1 UBC ELK1 RBMXL2 UBB JUND CNR1 MELK PPP1R3A SUMO2 ERCC4 BRCA1 LMO7 MDM2 NBR1 PMS1 IGF1R TOPBP1 TUBA4A UBA52 PPT1 CSTF1 SMARCA4 RNF168 JUNB TERF2 PPM1D DHFR CDK16 FBXO25 SMARCC1 SMARCD2 NCOA3 FAM175B BRCA1 STK11 MED13 WHSC2 CREB1 SMAD3 E2F4 RBBP7 CHD8 ERBB2 BRE HDAC2 WWP1 TP53 LMO4 FANCC KIAA1182 RAD17 EP300 BRAP CDK2 FANCE NUFIP1 DCUN1D1 HIST1H4A PMS2 RNF53 BARD1 POLL RBBP8 BRCC1 FANCL FGFR2 CLSPN RFC1 BRCA1 NBR2 MYC FANCF SMAD1 TFDP2 GTF2H4 DCLRE1C MAP3K3 RAD54B DDB2 BRIP1 RBBP4 BAP1 RAD51 DPPA3 AR FBXO9 NFYA RNF11 ZCCHC8 C5orf4 PSMC3IP
  9. 9. 9
  10. 10. 10
  11. 11. Introduction to Biological Network Analysis Using Cytoscape 11
  12. 12. Network? 12
  13. 13. Human Interactome data from BioGRID visualized by Cytoscape
  14. 14. Twitter Visualization
  15. 15. Network of Networks M6 M2 M17 M1 M8 M9 M4 M10 M14 M3 M5 M7 M11 M16 M19 M18 M13 M20 M15 15 M12
  16. 16. Human-Curated Pathways 16
  17. 17. Network = Nodes + Edges 17
  18. 18. Nodes and Edges in Biology Node - Protein - Protein - Protein - DNANode Edge - Genetic (Epistasis) - Synthetic lethality - Biochemical Reactions - Compound - Enzyme - Compound 18 Cartoon representation of a complex between DNA and the protein p53
  19. 19. Undirected Network- Protein - Protein Interaction19
  20. 20. Directed NetworkKEGG Pathway (TCA Cycle) visualized by Cytoscape KGMLReader 20
  21. 21. KEGG Global Map Visualized by Cytoscape 21
  22. 22. Cytoscape Workflow1.Load Networks (Get network data)‫‏‬2.Load Attributes (Get data about networks)‫‏‬3.Analyze and Visualize Networks4.Prepare for Publication - A specific example of this workflow: − Cline, et al. “Integration of biological networks and gene expression data using Cytoscape”, Nature Protocols, 2, 2366-2382 (2007). 22
  23. 23. Network Data Attributes Apps Annotated Networks Analyzed Data
  24. 24. <?xml version="1.0" encoding="UTF-8"?><graphml xmlns="http://graphml.graphdrawing.org/xmlns" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd"><!-- Created by igraph --> <key id="degree" for="node" attr.name="degree" attr.type="double"/> <key id="betweenness" for="node" attr.name="betweenness" attr.type="double"/> <graph id="G" edgedefault="directed"> <node id="n0"> <data key="degree">79</data> <data key="betweenness">0</data> </node> <node id="n1"> <data key="degree">9</data> <data key="betweenness">167</data> </node> <node id="n2"> <data key="degree">18</data> <data key="betweenness">75</data> </node> <node id="n3"> <data key="degree">8</data> <data key="betweenness">12</data> </node> <node id="n4"> <data key="degree">26</data> <data key="betweenness">210</data> </node> <node id="n5"> <data key="degree">29</data> Import Networks <data key="betweenness">320</data> </node> 24
  25. 25. Network Data Formats - SIF - GML - Excel - XGMML - Delimited Text - GraphML Table - BioPAX - CSV - PSI-MI - Tab - SBML - KGML (KEGG) 25
  26. 26. I Don’t Have a Network!- Don’t worry - There are tons of public interaction data sets - Cytoscape can import those public data sets directly via Internet. 26
  27. 27. Which Database?- Protein - Protein - STRING, IntAct- Genetic - BioGRID- Protein - Compound - ChEMBL- Human-Curated Pathways - KEGG, Reactome, PathwayCommons 27
  28. 28. PSICQUIC - Standardized mechanism to access public interaction data sets - In short, you can search multiple databases at once 28
  29. 29. Import Attributes 29
  30. 30. What are Attributes?- Any data that describes or provides details about nodes, edges, and networks. 30
  31. 31. GO Terms: DNA Repair NCBI Gene ID 672 Cell Cycle DNA Binding BRCA1 Ensemble IDOn Chromosome 17 ENSG00000012048 31
  32. 32. Why we need attributes?- Analysis - It is hard to get biologically meaningful analysis result only from network topology (= structure)- Meaningful Visualization - Expression values - Node Color - Gene Function - Node Shape - etc. 32
  33. 33. Node Attributes- Gene Expression Data- Human-readable gene names- Gene Ontology Terms 33
  34. 34. Edge Attributes- Interaction Detection Methods - Y2H, NMR, affinity chromatography, etc.- Interaction Type - Physical, genetic, predicted- Publication ID 34
  35. 35. Network Attributes - Experiment details - Pathway Metadata - Description - Publication ID 35
  36. 36. Public Data Source - Access directly from Cytoscape, or - Import as Table (Text/Excel) 36
  37. 37. Mapping Key in the NetworkMapping Key in the Table 37
  38. 38. Analysis 38
  39. 39. Network Analysis - Analysis is a huge topic in Cytoscape, so I’ll show you only the very basic features only.- Filtering- Calculate network statistics by Network Analyzer - Degree distribution,centrality, etc.- Advanced analysis by Apps 39
  40. 40. Filtering- Find nodes and edges with specific conditions - Pick nodes with degree > 5 - Select edges extracted from publication X - Find nodes annotated by GO term ID Y 40
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  44. 44. Visualization44
  45. 45. ?45
  46. 46. Layouts 46
  47. 47. Biological Data Visualization- Help others to understand your data- Emphasize what you want to tell by the image テキスト - Use color, shape, size of objects effectively! - Tamara Munzner Web Site: http://www.cs.ubc.ca/~tmm/ 47
  48. 48. Visual Style - Collection of mappings from Attributes to Visual Properties48
  49. 49. Default View Editor Discrete Mapping EditorContinuous Mapping Editor 49
  50. 50. 50
  51. 51. 51
  52. 52. 52
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  54. 54. 54
  55. 55. Prepare for Publication- Network images can be exported as PDF/ PS/PNG/JPG.- Use PDF for your publications 55
  56. 56. Real World Examples http://cytoscape-publications.tumblr.com 56
  57. 57. Expanding Cytoscape with Apps57
  58. 58. Cytoscape Apps- Were called Plugins- Add new features to Cytoscape- Large app developer/user community - This is the reason why Cytoscape is so popular! 58
  59. 59. http://apps.cytoscape.org 59
  60. 60. AllegroMCODE APCluster APID2NET BioQualiPlugin BLAST2SimilarityGraph BNMatch CABINCalculateNodeDegree CentiScaPe ChemViz clusterExplorerPlugin clusterMaker ClusterONEClusterViz COMA CommFinder CyClus3D CyOog cytoHubba Cytomcl DualLayoutdynamicXpr EnhancedSearch EnrichmentMap ExprEssence GraMoFoNe GraphletCounterHiderSlider jActiveModules mcl-new MCODE MINE NeMo NetAtlas NetCirChro netMatchNetworkAnalyzer NetworkEvolution OmicsAnalyzer OmicsViz OrthoNets PanGIAPerturbationAnalyzer PinnacleZ RandomNetworks RDFScsape Reactome FIsRemainingDegreeDistribution ReOrientPlugin ShortestPath Plugin SimTrek structureVizTransClust VennDiagramGenerator VistaClaraPlugin WordCloud BiNoM bioCycPluginBiogridPlugin BiomartClient BioNetBuilder BisoGenet ConsensusPathDBplugin 140+ AppsCoryneRegNetLoader CyThesaurus-ID-Mapping CytoSQL DroID Genoscape GPML-PluginGraphMLReader IntActWSClient iRefScape KGMLReader MetScape MiMIplugin NCBIClientNCBIEntrezGeneUserInterface Pathintegrator PhosphositePlus Web Service Client ModulePICRClient PSICQUICUniversalClient ReConn SessionForWeb SFLDLoader StringWSClientSuperpathways-Plugin 3DScape AgilentLiteratureSearch Cytoprophet DisGeNETDomainGraph ExpressionCorrelation GeneMANIA MetaNetter MONET BiNGO BubbleRouterClueGO CommonAttributes DisplayNetworkFromFlatFile FluxViz FunNetViz HyperEdgeEditorPiNGO CyGoose CytoscapeRPC GroovyScriptingEngine JavaScriptEngine MiSinkPythonScriptingEngine RubyScriptingEngine ScriptEngineManager addParentNeighborsAdvancedNetworkMerge batchTool BiLayout commandTool coreCommands CyAnimatoredgeLengthPlugin edgeLister EpiTrace FERN FM3 GoogleChartFunctions GroupToolMetaNodePlugin2 MultilevelLayoutPlugin NamedSelection NatureProtocolsWorkflowNeighborHighlight NetLink nodeCharts PhyloTree VennDiagrams
  61. 61. A Must ReadA travel guide to Cytoscape pluginsRintaro Saito, Michael E Smoot, Keiichiro Ono, Johannes Ruscheinski, Peng-Liang Wang, Samad Lotia, Alexander R Pico, Gary D Bader, Trey Ideker(2012)Nature Methods 9 (11) p. 1069-1076 61
  62. 62. Advanced Topics 62
  63. 63. Custom Graphics 63
  64. 64. Nested Networks 64
  65. 65. Upcoming Projects 65
  66. 66. - Cytoscape 3 3- Integration to Web 66
  67. 67. HUGE UpdateC2 3 67
  68. 68. 68
  69. 69. What’s New in 3?- New Visualization features - Edge Bend, Background Images- Server-side applications- Headless Mode (Command-line)- More advanced visualization by new rendering engines- For developers: Cleaner API 69
  70. 70. Release Schedule- User Beta - available now- 3.0 Final Release - At Cytoscape Retreat 2012 @UCSF - December 13, 14 - For more information, please visit: http://www.cytoscape.org/cy3.html 70
  71. 71. cytoscape.js- JavaScript version of Cytoscape for network visualization on the web browsers- Subset of Cytoscape functions- Will be integrated more to Cytoscape 3! 71
  72. 72. 72
  73. 73. 73
  74. 74. Getting Help- Two Google Groups - cytoscape-discuss@googlegroups.com - cytoscape-helpdesk@googlegroups.com- ANY question is OK! 74
  75. 75. P41 RR031228 (NRNB)NIH GM070743-01 P01 HG005062 75
  76. 76. www.cytoscape.org

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