1. Hubba: Hub Objects Analyzer—A Framework of Interactome Hubs Identification for Network Biology 吳 信 宏, Hsin-Hung Wu eastc228@iis.sinica.edu.tw Laboratory of System Biology and Network Biology Institute of Information Science, Academic Sinica Department of Computer Science and Information Engineering, NTU July 24, 2009

2. Outline Network Summary What Does Hubba Do Hubba Methods Web Demo & cyto-Hubba

3. Network Structure Network includes: Nodes Edges Node: Person 、 web page 、 station 、 destination Edge: Relationship 、 internet connection 、 traffic path

4. Traffic Network

5. World Wide Web

6. Human relationship

7. Protein interaction network Node → protein Edge → interaction Information inside a PPI network

8. What kind of information ?

9. Yeast Protein Interaction Network 1870 proteins 2240 interactions Barabási A. L. et al., Nature 2001 Hubs 、 pathways 、 complexes

10. What Does Hubba Do? A web-based service –http://hub.iis.sinica.edu.tw/Hubba/http://hub.iis.sinica.edu.tw/Hubba/ Exploring the essential nodes by 6 methods –Each method gives one score (rank) to each protein Visualizing the results in a user-friendly mode –Subgraph –First-level neighbors –Shortest path among proteins

11. Concept of Hubba Hubba ComplexPathway Hubs PPI networkSubnetwork

12. Hubba ( http://hub.iis.sinica.edu.tw/Hubba/) http://hub.iis.sinica.edu.tw/Hubba/

13. The Input Format PSI Tab-delimited Tab-delimited with weight

14. PSI

15. Tab-delimited The input : AB AC AD AG AH BA BC BF CA CB DA EF EH FB FG GA GF HA HE

16. Tab-delimited with weight The input : AB0.9 AC0.9 AD0.5 AG1 AH0.2 BA0.9 BC1 BF0.7 CA0.9 CB1 DA0.5 EF0.8 EH0.3 FB0.7 FG0.4 GA1 GF0.4 HA0.2 HE0.3 1 0.7 0.9 0.4 0.5 0.8 0.3 0.2 1

17. Algorithms (topological) Degree (2001) BottleNeck (2004, 2007) Edge Percolation Component (EPC) (2003) Subgraph Centrality (SC) (2006) Maximum Neighborhood Component (MNC) Density of Maximum Neighborhood Component (DMNC) Double Screening Scheme (DSS)

18. DSS in Hubba MNC and DMNC are selected: –Choose 2*n the top nodes in MNC –Rank the selected nodes (2*n) again in DMNC –Output the first n nodes (DSS result)

19. Cyto-Hubba http://www.cytoscape.org/ Hubba analysis Additional information Compute the Hubba Score Utilize Hubba with other plug-in

20. Now You Know.. Hubba helps you find out the essential candidates

21. Demo Hubba: –http://hub.iis.sinica.edu.tw/Hubba/http://hub.iis.sinica.edu.tw/Hubba/ cyto-Hubba: –http://hub.iis.sinica.edu.tw/cyto-Hubba/http://hub.iis.sinica.edu.tw/cyto-Hubba/