cytoscape workshop at salk 12/4/2012
DESCRIPTION
Presentation slides for Cytoscape Workshop at Salk 12/4/2012.TRANSCRIPT
CytoscapeAn Open Source Platform for Biological Network Analysis and Visualization
Keiichiro OnoCytoscape Core Developer TeamUniversity of California, San Diego
Trey Ideker Lab
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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
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Outline
- What is Cytoscape?
- How to Use Basic Features of Cytoscape
- Cytoscape 3 and Beyond3
What is Cytoscape?
Cytoscape
- Open source platform for biological network data integration, analysis, and visualization
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- Free! (LGPL)- Developed and maintained by
universities, companies, and research institutions
- De-facto standard software in biological network research community
- Expandable by Apps
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Introduction to Biological Network Analysis Using
Cytoscape11
Network?
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Human Interactome data from BioGRID visualized by Cytoscape
Twitter Visualization
M20
M10
M18
M9
M19
M12
M7
M6
M17M2
M15
M5M11
M4
M8M1
M3
M16
M13
M14
Network of Networks
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Human-Curated Pathways
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Network = Nodes + Edges
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Nodes and Edges in Biology
- Protein - Protein- Protein - DNA- Genetic (Epistasis)
- Synthetic lethality
- Biochemical Reactions
- Compound - Enzyme - Compound
Cartoon representation of a complex between DNA and the protein p53
Node
NodeEdge
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Undirected Network- Protein - Protein Interaction
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Directed Network
KEGG Pathway (TCA Cycle) visualized by Cytoscape KGMLReader20
KEGG Global Map Visualized by Cytoscape21
1.Load Networks (Get network data)2.Load Attributes (Get data about networks)3.Analyze and Visualize Networks 4.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).
Cytoscape Workflow
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Network Data
Annotated Networks
Attributes
Analyzed Data
Apps
<?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> <data key="betweenness">320</data> </node> Import Networks
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Network Data Formats- SIF
- GML
- XGMML
- GraphML
- BioPAX
- PSI-MI
- SBML
- KGML (KEGG)
- Excel
- Delimited Text Table
- CSV
- Tab
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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.
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Which Database?- Protein - Protein
- STRING, IntAct - Genetic
- BioGRID- Protein - Compound
- ChEMBL- Human-Curated
Pathways- KEGG, Reactome,
PathwayCommons27
PSICQUIC- Standardized
mechanism to access public interaction data sets
- In short, you can search multiple databases at once
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Import Attributes29
What are Attributes?
- Any data that describes or provides details about nodes, edges, and networks.
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BRCA1
NCBI Gene ID 672
On Chromosome 17
GO Terms:DNA RepairCell Cycle
DNA Binding
Ensemble ID ENSG00000012048
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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.
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Node Attributes
- Gene Expression Data
- Human-readable gene names
- Gene Ontology Terms
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Edge Attributes
- Interaction Detection Methods
- Y2H, NMR, affinity chromatography, etc.
- Interaction Type
- Physical, genetic, predicted
- Publication ID
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Network Attributes
- Experiment details
- Pathway Metadata
- Description
- Publication ID
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Public Data Source
- Access directly from Cytoscape, or
- Import as Table (Text/Excel)
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Mapping Key in the Network
Mapping Key in the Table
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Analysis38
Network Analysis
- Filtering- Calculate network statistics by
Network Analyzer- Degree distribution,centrality, etc.
- Advanced analysis by Apps
- Analysis is a huge topic in Cytoscape, so I’ll show you only the very basic features only.
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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
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Visualization
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?45
Layouts
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Biological Data Visualization
- Help others to understand your data
- Emphasize what you want to tell by the image
- Use color, shape, size of objects effectively!
- Tamara Munzner Web Site: http://www.cs.ubc.ca/~tmm/
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テキスト
Visual Style
- Collection of mappings from Attributes to Visual Properties
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Default View Editor
Discrete Mapping Editor
Continuous Mapping Editor
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Prepare for Publication
- Network images can be exported as PDF/PS/PNG/JPG.
- Use PDF for your publications
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Real World Examples
http://cytoscape-publications.tumblr.com
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Expanding Cytoscape with Apps57
Cytoscape Apps
- Were called Plugins- Add new features to Cytoscape- Large app developer/user community
- This is the reason why Cytoscape is so popular!
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http://apps.cytoscape.org
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AllegroMCODE APCluster APID2NET BioQualiPlugin BLAST2SimilarityGraph BNMatch CABIN CalculateNodeDegree CentiScaPe ChemViz clusterExplorerPlugin clusterMaker ClusterONE ClusterViz COMA CommFinder CyClus3D CyOog cytoHubba Cytomcl DualLayout dynamicXpr EnhancedSearch EnrichmentMap ExprEssence GraMoFoNe GraphletCounter HiderSlider jActiveModules mcl-new MCODE MINE NeMo NetAtlas NetCirChro netMatch NetworkAnalyzer NetworkEvolut ion OmicsAnalyzer OmicsViz OrthoNets PanGIA Per turbat ionAna lyzer P innac leZ RandomNetworks RDFScsape Reactome F Is RemainingDegreeDistribution ReOrientPlugin ShortestPath Plugin SimTrek structureViz TransClust VennDiagramGenerator VistaClaraPlugin WordCloud BiNoM bioCycPlugin Biogr idPlugin BiomartCl ient BioNetBui lder BisoGenet ConsensusPathDBplugin CoryneRegNetLoader CyThesaurus-ID-Mapping CytoSQL DroID Genoscape GPML-Plugin GraphMLReader IntActWSClient iRefScape KGMLReader MetScape MiMIplugin NCBIClient NCBIEntrezGeneUserInterface Pathintegrator PhosphositePlus Web Service Client Module PICRClient PSICQUICUniversalClient ReConn SessionForWeb SFLDLoader StringWSClient Superpathways-Plugin 3DScape Agi lentLiteratureSearch Cytoprophet DisGeNET DomainGraph ExpressionCorrelation GeneMANIA MetaNetter MONET BiNGO BubbleRouter ClueGO CommonAttributes DisplayNetworkFromFlatFile FluxViz FunNetViz HyperEdgeEditor PiNGO CyGoose CytoscapeRPC GroovyScriptingEngine JavaScriptEngine MiSink PythonScriptingEngine RubyScriptingEngine ScriptEngineManager addParentNeighbors AdvancedNetworkMerge batchTool BiLayout commandTool coreCommands CyAnimator edgeLengthPlugin edgeLister EpiTrace FERN FM3 GoogleChartFunctions GroupTool MetaNodePlugin2 Multi levelLayoutPlugin NamedSelection NatureProtocolsWorkflow NeighborHighlight NetLink nodeCharts PhyloTree VennDiagrams
140+ Apps
A Must Read
A 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
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Advanced Topics
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Custom Graphics63
Nested Networks64
Upcoming Projects
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- Cytoscape 3
- Integration to Web
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HUGE Update
C
2 367
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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
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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
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cytoscape.js
- JavaScript version of Cytoscape for network visualization on the web browsers
- Subset of Cytoscape functions- Will be integrated more to Cytoscape 3!
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NIH GM070743-01
P01 HG005062
P41 RR031228 (NRNB)
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