Hubba: Hub Objects Analyzer—A Framework of Interactome Hubs Identification for Network Biology 吳信宏, Hsin-Hung Wu Laboratory.

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Hubba: Hub Objects Analyzer—A Framework of Interactome Hubs Identification for Network Biology 吳信宏, Hsin-Hung Wu 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 、 station 、 destination Edge: Relationship 、 internet connection 、 traffic path

Traffic Network

World Wide Web

Human relationship

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 – 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 ComplexPathway Hubs PPI networkSubnetwork

Hubba (

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

PSI

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

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 HE

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-Hubba 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: – cyto-Hubba: –