CFinder: Locating cliques and overlapping modules in biological networks

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 http://angel.elte.hu/clustering. Contact: [email protected]

The free academic research software, CFinder, used for the publication is available at the website of the publication: http://angel.elte.hu/clustering

References in corpus (2)

• Uncovering the overlapping community structure of complex networks in nature and society
• Clique percolation in random networks

Cited by in corpus (7)

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• A sequential algorithm for fast clique percolation
• Evaluating Local Community Methods in Networks
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• Directed network modules
• Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae
• MOHCS: Towards Mining Overlapping Highly Connected Subgraphs