swMATH ID: 9080
Software Authors: Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T
Description: Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks. Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape’s software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.
Homepage: http://genome.cshlp.org/content/13/11/2498.short
Related Software: KEGG; R; IntAct; Bioconductor; Gephi; BioGRID; MetaCyc; NetworkX; igraph; UniProt; STRING; TRANSFAC; DAVID; Pajek; MCODE; BiNGO; DrugBank; GeneMANIA; CFinder; ClueGO
Referenced in: 41 Publications
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Referenced by 123 Authors

2 Kelemen, Arpad G.
2 Liang, Yulan
1 Ambroise, Christophe
1 Anbarasu, Anand
1 Bacic, Antony
1 Bag, Susmita
1 Baths, Veeky
1 Chang, Chang
1 Chen, Xinren
1 Cui, Yuehua
1 Curme, Chester
1 De Niz, Carlos
1 Delgado, Alberto Santos
1 Ding, Yanjun
1 Domico, Kelly
1 Dryden, Ian L.
1 Elloumi, Mourad
1 Fire, Michael
1 Galbraith, Sally
1 Golden, Bruce L.
1 Gollini, Isabella
1 Hashemi, Zahra Sadat
1 He, Dongxiao
1 Heath, Allison P.
1 Hinow, Peter
1 Hu, Guang
1 Huang, Chien-Hung
1 Indhumathy, M.
1 Jafarisani, Moslem
1 Jahangiri, Abolfazl
1 Jatana, Nidhi
1 Jin, Di
1 Kavraki, Lydia E.
1 Keith, Jonathan M.
1 Kelemen, Adam
1 Khalili, Saeed
1 Kinable, Joris
1 Kong, Yan
1 Latha, N.
1 Li, Gaoshi
1 Li, Hui
1 Li, Huijia
1 Li, Jianming
1 Li, Shaoyu
1 Li, Yaohang
1 Likić, Vladimir A.
1 Lithgow, Trevor
1 Liu, Chonghui
1 Liu, Chunmei
1 Liu, Dayou
1 Liu, Hsiang-Chuan
1 Liu, Hsueh-Chuan
1 Liu, Huaping
1 Lum, Oliver
1 Lv, Hongchao
1 Mahesh, K. B.
1 Martínez-Antonio, Agustino
1 Martinez de Aguiar, Marcus Aloizio
1 Mcconville, Malcolm J.
1 Michail, Dimitrios
1 Miele, Vincent
1 Moreira, Carolina A.
1 Murphy, Thomas Brendan
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1 Olivera, Beatriz Carely Luna
1 Omar, Sara Ibrahim
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1 Rahbar, Mohammad Reza
1 Rahman, Raziur
1 Rajendra, Rangaswamy
1 Ramaiah, Sudha
1 Rasaee, Mohammad Javad
1 Ren, Xianwen
1 Rietman, Edward A.
1 Salter-Townshend, Michael
1 Severn, Katie E.
1 Shen, Bairong
1 Sichi, John V.
1 Singh, Tarkeshwar
1 Singhal, Mudita
1 Song, Wei
1 Stanley, H. Eugene
1 Sun, Penggang
1 Tang, Chao
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