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

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/