1. Canadian Bioinformatics Workshops www.bioinformatics.ca

2. 2Module #: Title of Module

3. Module 3 Pathway and Network Analysis http://baderlab.org

4. Module 3: Pathway and Network Analysis bioinformatics.ca Network Visualization Outline Automatic network layout Visual features Visually interpreting a network

5. Module 3: Pathway and Network Analysis bioinformatics.ca Automatic network layout

6. Module 3: Pathway and Network Analysis bioinformatics.ca Automatic network layout Force-directed: nodes repel and edges pull Good for up to 500 nodes – Bigger networks give hairballs - Reduce number of edges Advice: try force directed first, or hierarchical for tree-like networks Tips for better looking networks – Manually adjust layout – Load network into a drawing program (e.g. Illustrator) and adjust labels

7. Focus Overview Zoom PKC Cell Wall Integrity

8. Module 3: Pathway and Network Analysis bioinformatics.ca Visual Features Node and edge attributes – String, integer, float, Boolean, list – E.g. represent gene, interaction attributes Visual attributes – Node, edge visual properties – Colour, shape, size, borders, opacity...

9. Module 3: Pathway and Network Analysis bioinformatics.ca Visual Features Guilt-by-association Dense clusters Global relationships

10. Module 3: Pathway and Network Analysis bioinformatics.ca Network Representations

11. Module 3: Pathway and Network Analysis bioinformatics.ca What Have We Learned? Automatic layout is required to visualize networks Networks help you visualize interesting relationships in your data Avoid hairballs by focusing analysis Visual attributes enable multiple types of data to be shown at once – useful to see their relationships

12. Module 3: Pathway and Network Analysis bioinformatics.ca Network Visualization/Analysis using Cytoscape Network visualization and analysis using Cytoscape software Cytoscape basics Cytoscape network analysis examples

13. Network visualization and analysis UCSD, ISB, Agilent, MSKCC, Pasteur, UCSF, Unilever, UToronto, U Texas http://cytoscape.org Pathway comparison Literature mining Gene Ontology analysis Active modules Complex detection Network motif search

14. Network Analysis using Cytoscape Databases Literature Expert knowledge Experimental Data Find biological processes underlying a phenotype Network Information Network Analysis

15. Manipulate NetworksFilter/Query Automatic Layout Interaction Database Search

16. Module 3: Pathway and Network Analysis bioinformatics.ca Active Community Help – 8 tutorials, >10 case studies – Mailing lists for discussion – Documentation, data sets Annual Conference: Ann Arbor July 18-20, 2010 10,000s users, 2500 downloads/month >60 Plugins Extend Functionality – Build your own, requires programming http://www.cytoscape.org Cline MS et al. Integration of biological networks and gene expression data using Cytoscape Nat Protoc. 2007;2(10):2366-82

17. Module 3: Pathway and Network Analysis bioinformatics.ca What Have We Learned? Cytoscape is a useful, free software tool for network visualization and analysis Provides basic network manipulation features Plugins are available to extend the functionality

18. Cytoscape Demo Version 2.6.3 www.cytoscape.org

19. Desktop Canvas Network overview Network manager Attribute browser CytoPanels FYI

20. yFiles Organic FYI

21. yFiles Circular FYI

22. Module 3: Pathway and Network Analysis bioinformatics.ca Network Layout 15 algorithms available through plugins Demo: Move, zoom/pan, rotate, scale, align FYI

23. Create Subnetwork FYI

24. Create Subnetwork FYI

25. Module 3: Pathway and Network Analysis bioinformatics.ca Visual Style Customized views of experimental data in a network context Network has node and edge attributes E.g. expression data, GO function, interaction type Mapped to visual attributes E.g. node/edge size, shape, colour… E.g. Visualize gene expression data as node colour gradient on the network FYI

26. Visual Style Load “Your Favorite Network” FYI

27. Visual Style Load “Your Favorite Expression” Dataset FYI

28. Visual Style Map expression values to node colours using a continuous mapper FYI

29. Visual Style Expression data mapped to node colours FYI

30. Module 3: Pathway and Network Analysis bioinformatics.ca Network Filtering FYI

31. Interaction Database Search FYI

32. Module 3: Pathway and Network Analysis bioinformatics.ca FYI

33. Module 3: Pathway and Network Analysis bioinformatics.ca FYI

34. Module 3: Pathway and Network Analysis bioinformatics.ca VistaClara Visualization for gene expression data Heat maps, sorting, animation

35. Module 3: Pathway and Network Analysis bioinformatics.ca Lab – Until 12:30pm Cytoscape – expression data visualization – Load the sample network file: galFiltered.sif – Lay it out – try different layouts – Load expression data - galExpData.pvals Use File->Import->Attribute from Table – Examine node attributes – Visualize gene expression data using the Visual Mapper – Install the VistaClara plugin from the plugin manager – Play the expression data as a movie

36. Module 3: Pathway and Network Analysis bioinformatics.ca Cytoscape 2.7, 2.8 Cytosape 2.7 is out now – Nested networks – Command line scripting Cytoscape 2.8 coming soon – Equations in attributes – Custom graphics

37. Module 3: Pathway and Network Analysis bioinformatics.ca We are on a Coffee Break & Networking Session