CFinder swMATH ID: 12379 Software Authors: Balázs Adamcsek; Gergely Palla; Illés J. Farkas; Imre Derényi; Tamás Vicsek Description: CFinder: locating cliques and overlapping modules in biological networks. 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. Supplementary information: Supplementary data are available on Bioinformatics online. Contact:cfinder@angel.elte.hu Homepage: http://bioinformatics.oxfordjournals.org/content/22/8/1021.short Related Software: MCODE; R; BioGRID; Cytoscape; KEGG; qgraph; CliquePercolationMethod-R; CliquePercolation; igraph; Pajek; STRING; PreSPI; NetworkX; miRBase; Biopython; LIBSVM; LabelRankT; RSiena; lda; PRMLT Cited in: 17 Documents all top 5 Cited by 52 Authors 2 Vicsek, Tamás 2 Zhang, Shihua 2 Zhang, Xiangsun 1 Batra, Amit 1 Birattari, Mauro 1 Chen, Bolun 1 Chen, Ling 1 Chen, Luonan 1 Dhawan, Sanjeev 1 Ekåioälu, Burak 1 Elloumi, Mourad 1 Gollini, Isabella 1 Gregory, Steve 1 Jabbour, Said 1 Jeon, Byeungwoo 1 Kasabov, Nikola K. 1 Kong, Yan 1 Liang, Jiye 1 Liu, Huaping 1 Liu, Wei 1 Ma, Liangyu 1 Mascia, Franco 1 Mhadhbi, Nizar 1 Mu, Junfang 1 Murphy, Thomas Brendan 1 Ning, Xuemei 1 Ozogány, Katalin 1 Palla, Gergely 1 Pellegrini, Paola 1 Perkins, Andy D. 1 Pirim, Harun 1 Raddaoui, Badran 1 Rasti, Saeid 1 Saïs, Lakhdar 1 Salter-Townshend, Michael 1 Singh, Kulvinder 1 Song, Wei 1 Stützle, Thomas G. 1 Tóth, Bálint C. 1 Vogiatzis, Chrysafis 1 Wang, Jiajia 1 Wang, Jie 1 Wang, Ruisheng 1 White, Arthur T. 1 Yin, Xia 1 Yu, Yang 1 Yüceer, Çetin 1 Zang, Weidong 1 Zhao, Xingwang 1 Zheng, Wenping 1 Zheng, Zeyu 1 Zomaya, Albert Y. all top 5 Cited in 11 Serials 3 Journal of Theoretical Biology 2 Journal of Statistical Physics 1 Computing 1 Information Sciences 1 Computers & Operations Research 1 Annals of Operations Research 1 International Transactions in Operational Research 1 New Journal of Physics 1 Computational Biology and Chemistry 1 Statistical Analysis and Data Mining 1 Springer Handbooks all top 5 Cited in 10 Fields 11 Biology and other natural sciences (92-XX) 4 Computer science (68-XX) 4 Game theory, economics, finance, and other social and behavioral sciences (91-XX) 2 General and overarching topics; collections (00-XX) 2 Combinatorics (05-XX) 2 Statistics (62-XX) 2 Operations research, mathematical programming (90-XX) 1 Mathematical logic and foundations (03-XX) 1 General topology (54-XX) 1 Statistical mechanics, structure of matter (82-XX) Citations by Year