Exploring overlapping functional units with various structure in protein interaction networks

PLoS ONE

Volumn 7, Issue 8, 2012, Pages

  Zhang, Xiao Fei ^a   Dai, Dao Qing ^a   Ou Yang, Le ^a   Wu, Meng Yun ^a  

^a SUN YAT SEN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ALGORITHM; ARTICLE; BIOLOGICAL FUNCTIONS; CONTROLLED STUDY; F SCORE; GOLD STANDARD; MEASUREMENT; MODEL; PROTEIN ANALYSIS; PROTEIN FAMILY; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; RECALL; REFERENCE DATABASE; REGULARIZED SPARSE RANDOM GRAPH MODEL; SACCHAROMYCES CEREVISIAE; TRANSLATION INITIATION;

ALGORITHMS; DATABASES, PROTEIN; MODELS, THEORETICAL; PROTEIN INTERACTION MAPS; SACCHAROMYCES CEREVISIAE;

EID: 84865195898     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0043092     Document Type: Article

References (45)

1. Barabási AL, Oltvai ZN, ((2004)) Network biology: understanding the cell's functional organization. Nat Rev Genet 5:: 101--113.
2. Spirin V, Mirny L, ((2003)) Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci USA 100:: 12123--12128.
3. Sharan R, Ulitsky I, Shamir R, ((2007)) Network-based prediction of protein function. Mol Syst Biol 3:: 88.
4. Li X, Wu M, Kwoh CK, Ng SK, ((2010)) Computational approaches for detecting protein complexes from protein interaction networks: a survey. BMC Genomics 11:: S3.
5. Enright AJ, Dongen SV, Ouzounis CA, ((2002)) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 30:: 1575--1584.
6. Bader GD, Hogue CW, ((2003)) An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 4:: 2.
7. King A, Pržulj N, Jurisica I, ((2004)) Protein complex prediction via cost-based clustering. Bioinformatics 20:: 3013--3020.
8. Jiang P, Singh M (2010) Spici: a fast clustering algorithm for large biological networks. Bioinformatics 26: 1105 - 1111.
9. Gillis J, Pavlidis P, ((2011)) The impact of multifunctional genes on "guilt by association" analysis. PloS One 6:: e17258.
10. Zhang XF, Dai DQ, ((2012)) A framework for incorporating functional inter-relationships into protein function prediction algorithms. IEEE/ACM Trans Comput Biol Bioinform 9:: 740--753.
11. Adamcsek B, Palla G, Farkas I, Derényi I, Vicsek T, ((2006)) Cfinder: locating cliques and overlapping modules in biological networks. Bioinformatics 22:: 1021--1023.
12. Cho Y, Hwang W, Ramanathan M, Zhang A, ((2007)) Semantic integration to identify overlapping functional modules in protein interaction networks. BMC Bioinformatics 8:: 265.
13. Liu G, Wong L, Chua H, ((2009)) Complex discovery from weighted ppi networks. Bioinformatics 25:: 1891--1897.
14. Rhrissorrakrai K, Gunsalus KC, ((2011)) Mine: module identification in networks. BMC Bioinformatics 12:: 192.
15. Becker E, Robisson B, Chapple C, Guénoche A, Brun C, ((2012)) Multifunctional proteins revealed by overlapping clustering in protein interaction network. Bioinformatics 28:: 84--90.
16. Nepusz T, Yu H, Paccanaro A, ((2012)) Detecting overlapping protein complexes in protein-protein interaction networks. Nat Methods 9:: 471--472.
17. Zhang XF, Dai DQ, Li XX, ((2012)) Protein complexes discovery based on protein-protein interaction data via a regularized sparse generative network model. IEEE/ACM Trans Comput Biol Bioinform 9:: 857--870.
18. Luo F, Yang Y, Chen CF, Chang R, Zhou J, et al. ((2007)) Modular organization of protein interaction networks. Bioinformatics 23:: 207--214.
19. Ahn Y, Bagrow J, Lehmann S, ((2010)) Link communities reveal multiscale complexity in networks. Nature 466:: 761--764.
20. Wang Z, Zhang J, ((2007)) In search of the biological significance of modular structures in protein networks. PLoS Comput Biol 3:: e107.
21. Pinkert S, Schultz J, Reichardt J, ((2010)) Protein interaction networks-more than mere modules. PLoS Comput Biol 6:: e1000659.
22. Jiao Q, Zhang Y, Li L, Shen H, ((2011)) Bintree seeking: a novel approach to mine both bi-sparse and cohesive modules in protein interaction networks. PLoS One 6:: e27646.
23. Fortunato S, Barthelemy M, ((2007)) Resolution limit in community detection. Proc Natl Acad Sci USA 104:: 36--41.
24. Qi Y, Balem F, Faloutsos C, Klein-Seetharaman J, Bar-Joseph Z, ((2008)) Protein complex identification by supervised graph local clustering. Bioinformatics 24:: i250--i258.
25. Higham D, Rašajski M, Pržulj N, ((2008)) Fitting a geometric graph to a protein-protein interaction network. Bioinformatics 24:: 1093--1099.
26. Schweiger R, Linial M, Linial N, ((2011)) Generative probabilistic models for protein-protein interaction networks-the biclique perspective. Bioinformatics 27:: i142--i148.
27. Saul Z, Filkov V, ((2007)) Exploring biological network structure using exponential random graph models. Bioinformatics 23:: 2604--3611.
28. Clauset A, Moore C, Newman M, ((2008)) Hierarchical structure and the prediction of missing links in networks. Nature 453:: 98--101.
29. Kuchaiev O, Rašajski M, Higham D, Pržulj N, ((2009)) Geometric de-noising of protein-protein interaction networks. PLoS Comput Biol 5:: e1000454.
30. Ranola J, Ahn S, Sehl M, Smith D, Lange K, ((2010)) A poisson model for random multigraphs. Bioinformatics 26:: 2004--2011.
31. Newman M, Leicht E, ((2007)) Mixture models and exploratory analysis in networks. Proc Natl Acad Sci USA 104:: 9564--9569.
32. Ball B, Karrer B, Newman M, ((2011)) Efficient and principled method for detecting communities in networks. Phys Rev E 84:: e036103.
33. Lee DD, Seung HS (2001) Algorithms for non-negative matrix factorization. In: Adv Neural Inf Process Syst. volume 13, 556-562.
34. Gavin A, Aloy P, Grandi P, Krause R, Boesche M, et al. ((2006)) Proteome survey reveals modularity of the yeast cell machinery. Nature 440:: 631--636.
35. Krogan N, Cagney G, Yu H, Zhong G, Guo X, et al. ((2006)) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440:: 637--643.
36. Collins S, Kemmeren P, Zhao X, Greenblatt J, Spencer F, et al. ((2007)) Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae. Mol Cell Proteomics 6:: 439--450.
37. Stark C, Breitkreutz B, Reguly T, Boucher L, Breitkreutz A, et al. ((2006)) Biogrid: a general repository for interaction datasets. Nucleic Acids Res 34:: D535--D539.
38. Mewes H, Amid C, Arnold R, Frishman D, Gueldener U, et al. ((2004)) Mips: analysis and annotation of proteins from whole genomes. Nucleic Acids Res 32:: D41--D44.
39. Cherry J, Adler C, Ball C, Chervitz S, Dwight S, et al. ((1998)) SGD: Saccharomyces genome database. Nucleic Acids Res 26:: 73--79.
40. Brohée S, Van Helden J, ((2006)) Evaluation of clustering algorithms for protein-protein interaction networks. BMC Bioinformatics 7:: 488.
41. Ashburner M, Ball C, Blake J, Botstein D, Butler H, et al. ((2000)) Gene ontology: tool for the unification of biology. Nat Genet 25:: 25--29.
42. Xie Z, Kwoh C, Li X, Wu M, ((2011)) Construction of co-complex score matrix for protein complex prediction from ap-ms data. Bioinformatics 27:: i159--i166.
43. Song J, Singh M, ((2009)) How and when should interactome-derived clusters be used to predict functional modules and protein function? Bioinformatics 25:: 3143--3150.
44. Boyle E, Weng S, Gollub J, Jin H, Botstein D, et al. ((2004)) Termfinder-open source software for accessing gene ontology information and finding significantly enriched gene ontology terms associated with a list of genes. Bioinformatics 20:: 3710--3715.
45. Cline M, Smoot M, Cerami E, Kuchinsky A, Landys N, et al. ((2007)) Integration of biological networks and gene expression data using cytoscape. Nat Protoc 2:: 2366--2382.