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Article; Bioinformatics

GECluster: a novel protein complex prediction method

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Pages 753-761 | Received 17 Dec 2013, Accepted 26 May 2014, Published online: 17 Oct 2014

References

  • Zhang Y, Lin H, Yang Z, Wang J. Construction of ontology augmented networks for protein complex prediction. PloS One. 2013;8:e62077, 1–9.
  • Liu G, Wong L, Chua HN. Complex discovery from weighted PPI networks. Bioinformatics. 2009;25:1891–1897.
  • Bader GD, Hogue CW. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinform. 2003;4:2–29.
  • Liu CN, Li J, Zhao Y. Exploring hierarchical and overlapping modular structure in the yeast protein interaction network. BMC Genomics. 2010;11:17–29.
  • Clauset A, Moore C, Newman ME. Hierarchical structure and the prediction of missing links in networks. Nature. 2008;453:98–101.
  • Srihari S, Leong HW. A survey of computational methods for protein complex prediction from protein interaction networks. J Bioinform Comput Biol. 2013;11:1230002–1230029.
  • Zhang Y, Lin H, Yang Z, Wang J, Li Y, Xu B. Protein complex prediction in large ontology attributed protein-protein interaction networks. IEEE/ACM Trans Comput Biol Bioinform/IEEE. 2013;10:729–741.
  • Wang J, Xie D, Lin H, Yang Z, Zhang Y. Filtering gene ontology semantic similarity for identifying protein complexes in large protein interaction networks. Proteome Sci. 2012;10(Suppl 1):S18, 1–10.
  • Jin Y, Turaev D, Weinmaier T, Rattei T, Makse HA. The evolutionary dynamics of protein-protein interaction networks inferred from the reconstruction of ancient networks. PloS One. 2013;8:e58134, 1–15.
  • Chen B, Fan W, Liu J, Wu FX. Identifying protein complexes and functional modules – from static PPI networks to dynamic PPI networks. Brief Bioinform. 2014;15:177–194.
  • The Gene Ontology (GO) project in 2006. Nucleic Acids Res. 2006;34:D322–D326.
  • Wu M, Li XL, Kwoh CK, Ng SK. A core-attachment based method to detect protein complexes in PPI networks. BMC Bioinform. 2009;10:169–185.
  • Chua HN, Sung WK, Wong L. Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions. Bioinformatics. 2006;22:1623–1630.
  • Edgar R, Domrachev M, Lash AE. Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 2002;30:207–210.
  • Marks VD, Ho Sui SJ, Erasmus D, van der Merwe GK, Brumm J, Wasserman WW, Bryan J, van Vuuren HJ. Dynamics of the yeast transcriptome during wine fermentation reveals a novel fermentation stress response. FEMS Yeast Res. 2008;8:35–52.
  • Xenarios I, Fernandez E, Salwinski L, Duan XJ, Thompson MJ, Marcotte EM, Eisenberg D. DIP: The Database of Interacting Proteins: 2001 update. Nucleic Acids Res. 2001;29:239–241.
  • Li M, Chen JE, Wang JX, Hu B, Chen G. Modifying the DPClus algorithm for identifying protein complexes based on new topological structures. BMC Bioinform. 2008;9:398–414.
  • Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4:44–57.
  • Adamcsek B, Palla G, Farkas IJ, Derenyi I, Vicsek T. CFinder: locating cliques and overlapping modules in biological networks. Bioinformatics. 2006;22:1021–1023.
  • Brohee S, van Helden J. Evaluation of clustering algorithms for protein-protein interaction networks. BMC Bioinform. 2006;7:488–507.
  • Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, Marzioch M, Rau C, Jensen LJ, Bastuck S, Dumpelfeld B, Edelmann A, Heurtier MA, Hoffman V, Hoefert C, Klein K, Hudak M, Michon AM, Schelder M, Schirle M, Remor M, Rudi T, Hooper S, Bauer A, Bouwmeester T, Casari G, Drewes G, Neubauer G, Rick JM, Kuster B, Bork P, Russell RB, Superti-Furga G. Proteome survey reveals modularity of the yeast cell machinery. Nature. 2006;440:631–636.
  • Chakraborty S, Ghosh TC. Evolutionary rate heterogeneity of core and attachment proteins in yeast protein complexes. Genome Biol Evol. 2013;5:1366–1375.
  • Das J, Chakraborty S, Podder S, Ghosh TC. Complex-forming proteins escape the robust regulations of miRNA in human. FEBS Lett. 2013;587:2284–2287.
  • Chakraborty S, Kahali B, Ghosh TC. Protein complex forming ability is favored over the features of interacting partners in determining the evolutionary rates of proteins in the yeast protein-protein interaction networks. BMC Syst Biol. 2010;4:155–164.