CFinder: locating cliques and overlapping modules in biological networks

TLDR

Cellular functions are carried out by modules of densely interconnected proteins that often overlap, forming a network of modules within protein association networks. The authors present CFinder, a fast program for locating and visualizing overlapping, densely interconnected groups of nodes in undirected graphs, enabling navigation between the original graph and the web of these groups. CFinder locates and visualizes overlapping, densely interconnected groups of nodes in undirected graphs and lets users navigate between the original graph and the web of these groups. CFinder predicts protein functions and discovers novel modules in gene/protein association networks, and efficiently locates cliques in large sparse graphs. CFinder and its manual are available for Windows, Linux, and Macintosh, with supplementary data online and contact at [e-mail].

Abstract

Abstract Summary: Most cellular tasks are performed not by individual proteins, but by groups of functionally associated proteins, often referred to as modules. In a protein assocation network modules appear as groups of densely interconnected nodes, also called communities or clusters. These modules often overlap with each other and form a network of their own, in which nodes (links) represent the modules (overlaps). We introduce CFinder, a fast program locating and visualizing overlapping, densely interconnected groups of nodes in undirected graphs, and allowing the user to easily navigate between the original graph and the web of these groups. We show that in gene (protein) association networks CFinder can be used to predict the function(s) of a single protein and to discover novel modules. CFinder is also very efficient for locating the cliques of large sparse graphs. Availability: CFinder (for Windows, Linux and Macintosh) and its manual can be downloaded from . Supplementary information: Supplementary data are available on Bioinformatics online. Contact: [e-mail]