CFinder: locating cliques and overlapping modules in biological networks

By Balázs Adamcsek, G. Palla, Illés J. Farkas, Imre Derényi, Tamás Vicsek. Bioinform., 2006

491 citations recorded by the source corpus.

UNLABELLED Most cellular tasks are performed not by individual proteins, but by groups of functionally associated proteins, often referred to as modules. In a protein association 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. SUPPLEMENTARY INFORMATION Supplementary data are available on Bioinformatics online.

Subfields: Biophysics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/83f47af18f74e131e5d6933195f3ab0f11c922ca

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Citations in the corpus

A survey of community search over big graphs (2019, methodology): “There is a maximal (3 , 2)-persistent-core interval [1 , 5] for the subgraph C induced by vertices { v 1 , v 2 , v 3 } .”
An analysis of parameter adaptation in reactive tabu search (2014, background): “2 [1, 15] \ {14} p hat300-3 15.”
Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review (2012, background): “…http://www.celldesigner.org Kitano et al., 2005 Cell Illustrator http://www.cellillustrator.com Nagasaki et al., 2011 CFinder http://www.cfinder.org Adamcsek et al., 2006 Cytoscape http://www.cytoscape.org Smoot et al., 2011 GenePro http://wodaklab.org/genepro Vlasblom et al., 2006 GeneWays…”
Community detection in graphs (2009, methodology): “Palla and coworkers (Adamcsek et al., 2006) have designed a software package implementing the CPM, called CFinder, which is freely available (www.cfinder.org).”
Community detection in social networks (2016, methodology): “CFinder 98 software was developed using CPM for overlapping community detection.”
Network-based prediction of protein function (2007, methodology): “Only a handful, such as MCODE (Bader and Hogue, 2003), PRODISTIN (Baudot et al , 2006), CFinder (Adamcsek et al , 2006) and NetworkBlast (http://www.pathblast.org/), are currently supported with a graphical interface.”
Detecting overlapping protein complexes in protein-protein interaction networks (2012, methodology): “2 CFinder CFinder [12, 13] was one of the first overlapping clustering methods published in the literature.”