1. Discussion summary Cytoscape introduction

2. 27803::Systems Biology2CBS, Department of Systems Biology

3. 27803::Systems Biology3CBS, Department of Systems Biology Sub-cellular localization coverage

4. 27803::Systems Biology4CBS, Department of Systems Biology Co-localization of interacting proteins

5. 27803::Systems Biology5CBS, Department of Systems Biology Tendency to interact with your cousin

6. 27803::Systems Biology6CBS, Department of Systems Biology Over-representation of highly abundant proteins

7. 27803::Systems Biology7CBS, Department of Systems Biology Coverage versus Accuracy say a lot, of which most is wrong say a lot, of which most is right say little, of which most is wrong say little, of which most is right Specificity Sensitivity

8. Visualizing protein relationships A short introduction to Cytoscape

9. 27803::Systems Biology9CBS, Department of Systems Biology Outline Visualization Why Cytoscape? Getting started User defined networks Attributes for nodes and edges

10. 27803::Systems Biology10CBS, Department of Systems Biology

11. 27803::Systems Biology11CBS, Department of Systems Biology

12. 27803::Systems Biology12CBS, Department of Systems Biology Visualization Systems Biology - looking at a system –a collection of units (gene/proteins) in a context Massive amounts of protein/gene relationships –a lot of undiscovered biology is hiding in that data –impossible to get an overview if investigated by hand Integrate many types of relationships –the data is available in the CBS data warehouse

13. 27803::Systems Biology13CBS, Department of Systems Biology

14. 27803::Systems Biology14CBS, Department of Systems Biology Why Cytoscape? www.cytoscape.org –can visualize relationships –is easy to use –has an advanced color coding scheme –allows for custom made plug-ins –has a strong community –is free for academia

15. 27803::Systems Biology15CBS, Department of Systems Biology Getting started Types of input formats –Tables of interactions (tab-delimited) –SIF: a simple input format Nodes: genes/proteins and their data (node attributes) Edges: node relationships and their data (edge attributes) are specified in another file

16. 27803::Systems Biology16CBS, Department of Systems Biology SIF example PPI in yeast YDL224C pp YER059W YDL224C pp YIL050W YDL224C pp YML064C YDL224C pp YNL189W YDR386W pp YBR009C YDR386W pp YBR098W YDR386W pp YCL032W YDR386W pp YDL043C YDR386W pp YDL208W YDR386W pp YDR363W YDR386W pp YDR381W YDR386W pp YER006W