Clust&See: A Cytoscape plugin for the identification, visualization and manipulation of network clusters

BioSystems

Volumn 113, Issue 2, 2013, Pages 91-95

  Spinelli, Lionel ^a,d   Gambette, Philippe ^a,d,f   Chapple, Charles E ^b,d   Robisson, Benoît ^b,d   Baudot, Anaïs ^a,d   Garreta, Henri ^c,d   Tichit, Laurent ^a,d   Guénoche, Alain ^a,d   Brun, Christine ^b,d,e  

^a AIX MARSEILLE UNIVERSITÉ   (France)

^b Aix Marseille university   (France)

^c AIX MARSEILLE UNIV   (France)

^d AIX MARSEILLE UNIVERSITY   (France)

^e CNRS   (France)

^f UNIVERSITÉ PARIS EST   (France)

Author keywords

Clustering; Graph partitioning; Interaction networks; Visualization

Indexed keywords

ALGORITHM; BIOINFORMATICS; GRAPHICAL METHOD; IDENTIFICATION METHOD; PERFORMANCE ASSESSMENT; SOFTWARE;

ALGORITHM; ARTICLE; CELL SURFACE; CLUSTER ANALYSIS; COMPUTER PROGRAM; CONTINGENCY TABLE; PERFORMANCE; PROTEIN ANALYSIS; PROTEIN INTERACTION;

EID: 84879563402     PISSN: 03032647     EISSN: 18728324     Source Type: Journal    
DOI: 10.1016/j.biosystems.2013.05.010     Document Type: Article

References (15)

1. Ahn Y.-Y., Bagrow J.P., Lehmann S. Link communities reveal multiscale complexity in networks. Nature 2010, 466:761-764.
2. Aittokallio T., Schwikowski B. Graph-based methods for analysing networks in cell biology. Brief Bioinform. 2006, 7:243-255.
3. Bader G.D., Hogue C.W. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinform. 2003, 4:2.
4. Becker E., Robisson B., Chapple C.E., Guénoche A., Brun C. Multifunctional proteins revealed by overlapping clustering in protein interaction network. Bioinformatics 2012, 28:84-90.
5. Gambette P., Guénoche A. Bootstrap clustering for graph partitioning. RAIRO - Oper. Res. 2012, 45:339-352.
6. Guénoche A. Consensus of partitions: a constructive approach. Adv. Data Anal. Classification 2011, 5:215-229.
7. Jaccard P. Distribution de la flore alpine dans le bassin des Dranses et de quelques régions voisines. Bull. Soc. Vaud. Sci. Nat. 1901, 37:241-272.
8. Kalinka A.T., Tomancak P. linkcomm: an R package for the generation, visualization, and analysis of link communities in networks of arbitrary size and type. Bioinformatics 2011, 27:2011-2012.
9. Kimbung S., Biskup E., Johansson I., Aaltonen K., Ottosson-Wadlund A., Gruvberger-Saal S., Cunliffe H., Fadeel B., Loman N., Berglund P., et al. Co-targeting of the PI3K pathway improves the response of BRCA1 deficient breast cancer cells to PARP1 inhibition. Cancer Lett. 2012, 319:232-241.
10. Morris J.H., Apeltsin L., Newman A.M., Baumbach J., Wittkop T., Su G., Bader G.D., Ferrin T.E. clusterMaker: a multi-algorithm clustering plugin for Cytoscape. BMC Bioinform. 2011, 12:436.
11. Nepusz T., Yu H., Paccanaro A. Detecting overlapping protein complexes in protein-protein interaction networks. Nat. Methods 2012, 9:471-472.
12. Newman M.E. Fast algorithm for detecting community structure in networks. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 2004, 69:066133.
13. Pilot-Storck F., Chopin E., Rual J.-F., Baudot A., Dobrokhotov P., Robinson-Rechavi M., Brun C., Cusick M.E., Hill D.E., Schaeffer L., et al. Interactome mapping of the phosphatidylinositol 3-kinase-mammalian target of rapamycin pathway identifies deformed epidermal autoregulatory factor-1 as a new glycogen synthase kinase-3 interactor. Mol. Cell Proteomics 2010, 9:1578-1593.
14. Shannon P., Markiel A., Ozier O., Baliga N.S., Wang J.T., Ramage D., Amin N., Schwikowski B., Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003, 13:2498-2504.
15. Slattery M.L., Lundgreen A., Herrick J.S., Wolff R.K. Genetic variation in RPS6KA1, RPS6KA2, RPS6KB1, RPS6KB2, and PDK1 and risk of colon or rectal cancer. Mutat. Res. 2011, 706:13-20.