Benchmarking Human Protein Complexes to Investigate Drug-Related Systems and Evaluate Predicted Protein Complexes

PLoS ONE

Volumn 8, Issue 2, 2013, Pages

  Wu, Min ^a   Yu, Qi ^b   Li, Xiaoli ^c   Zheng, Jie ^a   Huang, Jing Fei ^b   Kwoh, Chee Keong ^a  

^a NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

^b KUNMING INSTITUTE OF ZOOLOGY   (China)

^c INSTITUTE FOR INFOCOMM RESEARCH   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATE; DRUG BINDING PROTEIN; GELDANAMYCIN; GLUTAMIC ACID; GUANOSINE DIPHOSPHATE; IMATINIB; MANNOSE; MYRISTIC ACID; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE; PROTEIN;

ARTICLE; CATALOG HUMAN PROTEIN COMPLEX; COMPLEX FORMATION; COMPUTATIONAL FLUID DYNAMICS; DRUG PROTEIN BINDING; HUMAN; INSULIN DEPENDENT DIABETES MELLITUS; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN QUALITY; QUALITY CONTROL; DRUG INTERACTION; METABOLISM; PROCEDURES;

BENCHMARKING; DATABASES, PROTEIN; DRUG INTERACTIONS; HUMANS; PROTEIN INTERACTION MAPPING; PROTEINS;

EID: 84873533301     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0053197     Document Type: Article

References (45)

1. Schwarz DS, Tomari Y, Zamore PD, (2004) The rna-induced silencing complex is a mg2+-dependent endonuclease. Current Biology 14: 787-791.
2. Cramer P, Bushnell DA, Kornberg RD, (2001) Structural basis of transcription: RNA polymerase ii at 2.8 angstrom resolution. Science 292: 1844-1846.
3. Gosens I, den Hollander AI, Cremers FP, Roepman R, (2008) Composition and function of the crumbs protein complex in the mammalian retina. Experimental Eye Research 86: 713-726.
4. Wegener E, Krappmann D, (2008) Dynamic protein complexes regulate nf-kappab signaling. Handb Exp Pharmacol 186: 237-259.
5. Luc PV, Tempst P, (2004) Pindb: a database of nuclear protein complexes from human and yeast. Bioinformatics 20: 1413-1415.
6. Ruepp A, Brauner B, Dunger-Kaltenbach I, Frishman G, Montrone C, et al. (2008) Corum: the comprehensive resource of mammalian protein complexes. Nucleic Acids Research 36: 646-650.
7. Prasad TSK, Goel R, Kandasamy K, Keerthikumar S, Kumar S, et al. (2009) Human protein reference database- 2009 update. Nucleic Acids Research 37: 767-772.
8. Yang P, Li X, Wu M, Kwoh CK, Ng SK, (2011) Inferring gene-phenotype associations via global protein complex network propagation. PLOS ONE 6: e21502.
9. Goh WWB, Lee YH, Ramdzan ZM, Sergot MJ, Chung M, et al. (2012) Proteomics signature profiling (psp): A novel contextualization approach for cancer proteomics. J Proteome Res 11: 1571-1581.
10. Nacher JC, Schwartz JM, (2012) Modularity in protein complex and drug interactions reveals new polypharmacological properties. PLOS ONE 7: e30028.
11. Pu S, Wong J, Turner B, Cho E, Wodar SJ, (2009) Up-to-date catalogues of yeast protein complexes. Nucleic Acids Research 37: 825-831.
12. Begley CG, Ellis LM, (2012) Drug development: Raise standards for preclinical cancer research. Nature 483: 531-533.
13. Li J, Zhu X, Chen JY, (2009) Building disease-specific drug-protein connectivity maps from molecular interaction networks and PubMed abstracts. PLOS Computational Biology 5.
14. Lee HS, Bae T, Lee JH, Kim D, Oh Y, et al. (2012) Rational drug repositioning guided by an integrated pharmacological network of protein, disease and drug. BMC Systems Biology 6: 80.
15. Farkas IJ, Korcsmaros T, Kovacs IA, Mihalik A, Palotai R, et al. (2011) Network-based tools for the identification of novel drug targets. Science Signaling 4: pt3.
16. Yu Q, Li GH, Huang JF, (2012) Mofinder: A novel algorithm for detecting overlapping modules from protein-protein interaction network. J Biomed Biotechnol 2012: 103702.
17. Russ AP, Lampel S, (2005) The druggable genome: an update. Drug Discov Today 10: 1607-1610.
18. Clamp M, Fry B, Kamal M, Xie X, Cuff J, et al. (2007) Distinguishing protein-coding and noncoding genes in the human genome. PNAS 104: 19428-33.
19. Ashburn TT, Thor KB, (2004) Drug repositioning: identifying and developing new uses for existing drugs. Nat Rev Drug Discov 3: 673-83.
20. Jensen L, Saric J, Bork P, (2006) Literature mining for the biologist: from information retrieval to biological discovery. Nat Rev Genet 7: 119-129.
21. Agarwal P, Searls DB, (2008) Literature mining in support of drug discovery. Briefings in Bioinformatics 9: 479-492.
22. Louvet C, Szot GL, Lang J, Lee MR, Martinier N, et al. (2008) Tyrosine kinase inhibitors reverse type 1 diabetes in nonobese diabetic mice. PNAS 105: 18895-900.
23. Bader G, Hogue C, (2003) An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 4: 2.
24. Pereira-Leal JB, Enright AJ, Ouzounis CA, (2004) Detection of functional modules from protein interaction networks. PROTEINS:Structure, Function, and Bioinformatics 54: 49-57.
25. Altaf-Ul-Amin M, Shinbo Y, Mihara K, Kurokawa K, Kanaya S, (2006) Development and implementation of an algorithm for detection of protein complexes in large interaction networks. BMC Bioinformatics 7: 207.
26. Adamcsek B, Palla G, Farkas IJ, Derényi I, Vicsek T, (2006) Cfinder: locating cliques and overlapping modules in biological networks. Bioinformatics 22: 1021-1023.
27. Li X, Foo C, Ng S (2007) Discovering protein complexes in dense reliable neighborhoods of protein interaction networks. In: International Conference on Computational Systems Bioinformatics (CSB). pp. 157-168.
28. Li M, Chen J, Wang J, Hu B, Chen G, (2008) Modifying the dpclus algorithm for identifying protein complexes based on new topological structures. BMC Bioinformatics 9.
29. Wu M, Li XL, Kwoh CK, Ng SK, (2009) A core-attachment based method to detect protein complexes in ppi networks. BMC Bioinformatics 10: 169.
30. Liu GM, Chua HN, Wong L, (2009) Complex discovery from weighted ppi networks. Bioinformatics 25: 1891-1897.
31. Xie Z, Kwoh CK, Li X, Wu M, (2011) Construction of co-complex score matrix for protein complex prediction from ap-ms data. Bioinformatics 27: i159-i166.
32. Li XL, Wu M, Kwoh CK, Ng SK, (2010) Computational approaches for detecting protein complexes from protein interaction networks: A survey. BMC Genomics S1: S3.
33. Stark C, Breitkreutz BJ, Chatr-aryamontri A, Boucher L, Oughtred R, et al. (2011) The biogrid interaction database: 2011 update. Nucleic Acids Research 39: 698-704.
34. Chua HN, Ning K, Sung WK, Leong HW, Wong L, (2008) Using indirect protein-protein interactions for protein complex prediction. J Bioinformatics and Computational Biology 6: 435-466.
35. Brohee S, van Helden J, (2006) Evaluation of clustering algorithms for protein-protein interaction networks. BMC Bioinformatics 7: 488.
36. Wu M, Li X, Chua H, Kwoh CK, Ng SK, (2010) Integrating diverse biological and computational sources for reliable protein-protein interactions. BMC Bioinformatics 11(S7): S8.
37. Butte AJ, (2008) Translational bioinformatics: Coming of age. JAMIA 15: 709-714.
38. Lussier YA, Li H, (2012) The rise of translational bioinformatics. Genome Biology 13: 319.
39. Yan Q, (2010) Translational bioinformatics and systems biology approaches for personalized medicine. Methods Mol Biol 662: 167-178.
40. Bjornsson TD, Callaghan JT, Einolf HJ, Fischer V, Gan L, et al. (2003) The conduct of in vitro and in vivo drug-drug interaction studies: a phrma perspective. J Clin Pharmacol 43: 443-469.
41. Wang J, Du Z, Payattakool R, Yu P, Chen C, (2007) A new method to measure the semantic similarity of go terms. Bioinformatics 23: 1274-1281.
42. Johnson A, O'Donnell C, (2009) An open access database of genome-wide association results. BMC Medical Genetics 10: 6.
43. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, et al. (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci 106: 9362-9367.
44. Hu H, Yan X, Huang Y, Han J, Zhou XJ (2005) Mining coherent dense subgraphs across massive biological networks for functional discovery. In: ISMB (Supplement of Bioinformatics). pp. 213-221.
45. Knox C, Law V, Jewison T, Liu P, Ly S, et al. (2011) Drugbank 3.0: a comprehensive resource for 'omics' research on drugs. Nucleic Acids Research 39: 1035-1041.