BioPathways SIG, July.29.2004

1. BioPathways SIG, July.29.2004

2. Networks in Biology • Molecular interaction and similarity networks are vital for understanding gene function in biology • How does my gene of unknown function relate to a known gene? • Many biological questions can be answered by mapping the problem to a network problem www.cytoscape.org

3. Lots of Data to Analyze • Network data is accumulating • Protein-protein interactions, genetic pathways, metabolic networks, cell signals, gene regulations, similarity relationships, literature-based links • Software to view and query this information is required to efficiently answer scientific questions www.cytoscape.org

4. Network Visualization Tools • Pajek - Slovenia • Osprey - SLRI, Toronto • VisANT - BU • Biolayout - EBI • GraphViz • PowerPoint • Others • Cytoscape (only open-source biology) www.cytoscape.org

5. What is Cytoscape? • Cytoscape is a network visualization and analysis tool • An extensible platform for bioinformatics software development • New! 100% Open-source Java • GINY Graph Library • Version 2.0 released this week:www.cytoscape.org www.cytoscape.org

7. Example: Network Clustering • Clusters in a protein-protein interaction network have been shown to represent protein complexes and parts of pathways • Clusters in a protein similarity network represent protein families • Network clustering is available through the MCODE Cytoscape plugin www.cytoscape.org

8. Proteasome 26S Ribosome Proteasome 20S RNA Splicing RNA Pol core

9. Cytoscape Core Features • Visualize and lay out networks • Display network data using visual styles • Easily organize multiple networks • Bird’s eye view navigation of large networks • Supports SIF and GML, molecular profiling formats, node/edge attributes • Functional annotation from GO + KEGG • Metanodes (hyper graph / compound graph) • Extensible through plugins (20 developed) www.cytoscape.org

10. Layout • 16 algorithms available through plugins • Zooming, hide/show, alignment www.cytoscape.org

11. yFiles Organic

12. yFiles Circular

14. Visual Styles • Map graph attributes to visual attributes • Define visual styles for later use • Graph has node and edge attributes • E.g. expression data, interaction type, GO function • Mapped to visual attributes • E.g. node/edge size, shape, color, font… • Take continuous gene expression data and visualize it as continuous node colors www.cytoscape.org

15. Visual Styles Load “Your Favorite Network”

16. Visual Styles Load “Your Favorite Expression” Dataset

17. Visual Styles Map expression values to node colors using a continuous mapper

18. Visual Styles Expression data mapped to node colors

19. Visual Styles • Node attributes: node color, border color, border type, node shape, size, label, font • Edge attributes: edge color, line types, arrows, label, font • Multidimensional visual attribute mapping soon www.cytoscape.org

21. Filters • Multiple different filters are available • Arbitrary Boolean combinations www.cytoscape.org

22. What can you use it for? • Network visualization - multi-dimensional • Network-based molecular profiling analysis • Transcriptionally active network modules • Network clustering • Module and cluster detection • Network comparison • PathBLAST www.cytoscape.org

23. Network Analysis • Plugins for: • Networks and Transcriptional Profiling • Active Modules (UCSD) • Activity Centers (MSKCC) • Expression Data Viewers (ISB) • BioModules (ISB) • General network analysis • MCODE: network clustering (MSKCC) • PathBLAST (UCSD) • 10 published papers • >10 in development www.cytoscape.org

24. Data Access • Plugins for: • cPath / data services plugin (MSKCC) • Poster at main meeting • Recently available: • Control from Perl, Python, R (Cytotalk) • Data Cube Browser • BIND, PreBIND, HPRD access • Open architecture for plugin development www.cytoscape.org

25. Active Modules (UCSD) Ideker T, Ozier O, Schwikowski B, Siegel AF Bioinformatics. 2002;18 Suppl 1:S233-40

26. Active Modules

27. Biomodules (ISB) Prinz S, Avila-Campillo I, Aldridge C, Srinivasan A, Dimitrov K, Siegel AF, and Galitski T Genome Res. 2004 14: 380-390

28. cPath (MSKCC) www.cytoscape.org

29. Extensible • Architecture: 100% open source Java • Core + plugin API • Plugins are independently licensed • “Just need to write the algorithm” • Template code samples Plugin

30. Community • Mailing lists • cytoscape-announce@googlegroups.com • cytoscape-discuss@googlegroups.com • http://www.cytoscape.org • 100% open source • Contributions are encouraged www.cytoscape.org

31. MSK’s caBIG Pathway Plan • High-quality, non-redundant human pathways • Pathways (BioPAX)cPathCytoscape • BioPAX/PSI-MI represent pathway data • Pathway DBs + curation support standards • cPath merges BioPAX/PSI-MI datasets • Cytoscape analyses pathway datasets in context with other data e.g. gene expression • Query/retrieve caCORE information via plugin • Link with other caBIG groups/tools www.cytoscape.org

32. MSK’s caBIG Pathway Plan • High-quality, non-redundant human pathways • Pathways (BioPAX)cPathCytoscape • BioPAX/PSI-MI represent pathway data • Pathway DBs + curation support standards • cPath merges BioPAX/PSI-MI datasets • Cytoscape analyses pathway datasets in context with other data e.g. gene expression • Query/retrieve caCORE information via plugin • Link with other caBIG groups/tools www.cytoscape.org

33. Cytoscape Team Benno Schwikowski Hamid Bolouri Rowan Christmas Iliana Avila-Campillo Larissa Kamenkovich Andrew Markiel Paul Shannon Trey Ideker Nada Amin Ryan Kelley Dan Ramage Jonathan Wang Chris Workman Chris Sander Gary Bader Ethan Cerami Rob Sheridan www.cytoscape.org