Hubba: Hub Objects Analyzer—A Framework of Interactome Hubs Identification for Network Biology 吳...
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Transcript of Hubba: Hub Objects Analyzer—A Framework of Interactome Hubs Identification for Network Biology 吳...
Hubba: Hub Objects Analyzer—A Framework of Interactome Hubs Identification for Network Biology
吳 信 宏 , Hsin-Hung Wu [email protected]
Laboratory of System Biology and Network Biology
Institute of Information Science, Academic Sinica
Department of Computer Science and Information Engineering, NTU
July 24, 2009
Outline
• Network Summary
• What Does Hubba Do
• Hubba Methods
• Web Demo & cyto-Hubba
Network Structure
• Network includes:• Nodes• Edges
• Node:• Person、 web page 、 sta
tion、 destination
• Edge:• Relationship 、 internet co
nnection 、 traffic path
Traffic Network
World Wide Web
Human relationship
Protein interaction network
• Protein interaction network• Node → protein• Edge → interaction
Information inside a PPI network
What kind of information ?
Yeast Protein Interaction Network
• 1870 proteins• 2240 interactions
Barabási A. L. et al., Nature 2001
Hubs、 pathways、 complexes
What Does Hubba Do?
• A web-based service– 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
Concept of Hubba
Hubba
Complex Pathway
Hubs
PPI network Subnetwork
Hubba (http://hub.iis.sinica.edu.tw/Hubba/)
The Input Format
• PSI
• Tab-delimited
• Tab-delimited with weight
PSI
Tab-delimited The input :
A BA CA DA GA HB AB CB FC AC BD AE FE HF BF GG AG FH AH E
Tab-delimited with weight The input :
A B 0.9A C 0.9A D 0.5A G 1A H 0.2B A 0.9B C 1B F 0.7C A 0.9C B 1D A 0.5E F 0.8E H 0.3F B 0.7F G 0.4G A 1G F 0.4H A 0.2H E 0.3
1
0.7
0.9
0.9
0.4
0.5
0.8
0.30.2
1
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)
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)
Cyto-Hubbahttp://www.cytoscape.org/
Hubba analysis
Additional information
Compute the Hubba Score Utilize Hubba with other plug-in
Now You Know..
Hubba helps you find out the essential candidates
Demo
• Hubba:– http://hub.iis.sinica.edu.tw/Hubba/
• cyto-Hubba:– http://hub.iis.sinica.edu.tw/cyto-Hubba/