A hybrid graph-theoretic method for mining overlapping functional modules in large sparse protein interaction networks.
Modular architecture, which encompasses groups of genes/proteins involved in elementary biological functional units, is a basic form of the organisation of interacting proteins. Here, we propose a method that combines the Line Graph Transformation (LGT) and clique percolation-clustering algorithm to detect network modules, which may overlap each other in large sparse PPI networks. The resulting modules by the present method show a high coverage among yeast, fly, and worm PPI networks, respectively. Our analysis of the yeast PPI network suggests that most of these modules have well-biological significance in context of protein localisation, function annotation, and protein complexes.
Zhang
Shihua
S
Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China. zsh@amss.ac.cn
Liu
Hong-Wei
HW
Ning
Xue-Mei
XM
Zhang
Xiang-Sun
XS
D000465:Algorithms; D003628:Database Management Systems; D030562:Databases, Protein; D016247:Information Storage and Retrieval / Q000379:methods*; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*
D011506:Proteins