1. Biological networks Tutorial 12

2. Protein-Protein interactions –STRING Protein and genetic interactions –BioGRID Signaling pathways –SPIKE Network visualization –Cytoscape Biological networks

3. Protein Protein interactions (PPI)

7. Can also show regulatory relations

8. Protein Protein interactions (PPI)

12. Protein and genetic interactions

14. Signaling pathway networks

16. Signaling pathways Hearing and vision map

17. Network visualization - Cytoscape

18. Number of nodes Number of edges node edge

19. Network visualization - Cytoscape Analyzing the network

20. Network visualization - Cytoscape “Know your network type” Directed – for regulatory networks Undirected – for protein-protein networks

21. Network visualization - Cytoscape NetworkAnalyzer plug-in

22. Network visualization - Cytoscape Degree: the number of edges that a node has. The node with the highest degree in the graph

23. Network visualization - Cytoscape Closeness: measure how close a node to all other nodes in the network. The nodes with the highest closeness

24. Network visualization - Cytoscape The node with the highest betweenness Betweenness: quantify the number of all shortest paths that pass through a node.

25. Network visualization - Cytoscape

27. Highest degree = big Highest betweens = red

28. Network visualization - Cytoscape

29. Mcode plug-in

30. Network visualization - Cytoscape

31. Cytoscape has 140 (!) plug-ins