Hubba Hub Objects AnalyzerA Framework of Interactome Hubs

Hubba: Hub Objects Analyzer—A Framework of Interactome Hubs Identification for Network Biology 吳信宏, Hsin-Hung Wu eastc 228@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 、 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 Hubs、pathways、 complexes Barabási A. L. et al. , Nature 2001

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 Complex Pathway Hubba Hubs PPI network Subnetwork

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

The Input Format • PSI • Tab-delimited with weight

PSI

Tab-delimited The input : A A A B B B C C D E E F F G G H H B C D G H A C F A B A F H B G A F A E

Tab-delimited with weight The input : A A A B B B C C D E E F F G G H H B C D G H A C F A B A F H B G A F A E 0. 9 0. 5 1 0. 2 0. 9 1 0. 7 0. 9 1 0. 5 0. 8 0. 3 0. 7 0. 4 1 0. 4 0. 2 0. 3 0. 7 1 0. 9 0. 4 0. 8 1 0. 9 0. 5 0. 2 0. 3

Algorithms (topological) • Degree (2001) • Bottle. Neck (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)