Modular organization of protein interaction networks

• DOI: 10.1093/bioinformatics/btl562
• Publication Date: 2006-11-09T01:24:51Z
• Authors: Feng Luo; Yunfeng Yang; Chin-Fu Chen; Roger Chang; Jizhong Zhou; Richard H. Scheue...
• Keywords: 0301 basic medicine; 03 medical and health sciences; Saccharomyces cerevisiae Proteins; Protein Interaction Mapping; Computer Simulation; Saccharomyces cerevisiae; Models, Biological; Algorithms; Software; Signal Transduction

Accumulating evidence suggests that biological systems are composed of interacting, separable, functional modules. Identifying these modules is essential to understand the organization systems.In this paper, we present a framework identify within networks. In approach, concept degree extended from single vertex sub-graph, and formal definition module in network used. A new agglomerative algorithm was developed by combining with relative edge order generated Girvan-Newman (G-N) algorithm. JAVA program, MoNet, implement Applying MoNet yeast core protein interaction database interacting proteins (DIP) identified 86 simple sizes larger than three proteins. The obtained significantly enriched related process Gene Ontology terms. comparison between defined Radicchi et al. (2004) indicates show stronger co-clustering genes more robust ties betweenness values. Further, output retains adjacent relationships allows construction an web providing insight regarding different Thus, provides objective approach interactions processes cellular systems.MoNet available upon request authors.