Identifying protein complexes using hybrid properties

Journal of Proteome Research

Volumn 8, Issue 11, 2009, Pages 5212-5218

  Chen, Lei ^b,c   Shi, Xiaohe ^d   Kong, Xiangyin ^d   Zeng, Zhenbing ^c   Cai, Yu Dong ^a  

^a SHANGHAI UNIVERSITY   (China)

^b FUDAN UNIVERSITY   (China)

^c EAST CHINA NORMAL UNIVERSITY   (China)

^d SHANGHAI JIAO TONG UNIVERSITY SCHOOL OF MEDICINE   (China)

Author keywords

Feature selection; Jackknife cross validation test; mRMR(minimum redundancy maximum relevance); Nearest neighbor algorithm (NNA); Protein complex; Protein protein interaction (PPI)

Indexed keywords

PROTEIN DERIVATIVE;

ACCURACY; ALGORITHM; ARTICLE; COMPLEX FORMATION; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN PROTEIN INTERACTION;

ALGORITHMS; COMPUTATIONAL BIOLOGY; MULTIPROTEIN COMPLEXES; PROTEIN INTERACTION MAPPING; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SOFTWARE;

EID: 70449360607     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr900554a     Document Type: Article

References (37)

1. Qi, Y.; Balem, F.; Faloutsos, C.; Seetharaman, J. K.; Joseph, Z. B. Protein complex identification by supervised graph local clustering. Bioinformatics 2008, 24, 250-258.
2. Gavin, A. C. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 2002, 415, 141-147.
3. Ho, Y. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 2002, 415, 180-183.
4. Adamcsek, B.; Palla, G.; Farkas, I. J.; Derenyi, I.; Vicsek, T. CFinder: Locating cliques and overlapping modules in biological networks. Bioinformatics 2006, 22, 1021-1023.
5. Bader, G. D.; Hogue, C. W. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinf. 2003, 4, 2.
6. Zotenko, E.; Guimaraes, K. S.; Jothi, R.; Przytycka, T. M. Decomposition of overlapping protein complexes: A graph theoretical method for analyzing static and dynamic protein associations. Algorithms Mol. Biol. 2006, 1-7.
7. Spirin, V.; Mirny, L. A. Protein complexes and functional modules in molecular networks. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 12123-112118
8. King, A. D.; Przulj, N.; Jurisica, I. Protein complex prediction via cost-based clustering. Bioinformatics 2004, 20, 3013-3020. (Pubitemid 39619193)
9. Rives, A. W.; Galitski, T. Modular organization of cellular networks. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 1128-1133.
10. Chakrabarti, D. Tools for Large Graph Mining. Ph.D. Thesis, School of Computer Science, Carnegie Mellon University, 2005.
11. Barabasi, A. L.; Oltvai, Z. N. Network biology: understanding the cell's functional organization. Nat Rev Genet. 2004, 5, 101-103.
12. Stelzl, U.; Worm, U.; Lalowski, M.; Haenig, C.; Brembeck, F.; Goehler, H.; Stroedicke, M.; Zenkner, M.; Schoenherr, A.; Koeppen, S. A human protein-protein interaction network: a resource for annotating the proteome. Cell 2005, 122, 957-968.
13. Bock, J. R.; Gough, D. A. Predicting protein-protein interactions from primary structure. Bioinformatics 2001, 17 (5), 455-460.
14. Cai, C. Z.; Han, L. Y.; Ji, Z. L.; Chen, X.; Chen, Y. Z. SVM-Prot: web-based support vector machine software for functional classification of a protein from its primary sequence. Nucleic Acids Res. 2003, 31 (13), 3692-3697.
15. Cai, C. Z.; Wang, W. L.; Sun, L. Z.; Chen, Y. Z. Protein function classification via support vector machine approach. Math. Biol. Sci. 2003, 185 (2), 111-122. (Pubitemid 37108371)
16. Yu, X. J.; Cao, J. P.; Cai, Y. D.; Shi, T. L.; Li, Y. X. Predicting rRNA-,RNA-, and DNA-binding proteins from primary structure with support vector machines. J. Theor. Biol. 2006, 240 (2), 175-184.
17. Cherry, J. M.; Ball, C.; Weng, S.; Juvik, G.; Schmidt, R.; Adler, C.; Dunn, B.; Dwight, S.; Riles, L.; Mortimer, R. K.; Botstein, D. Genetic and physical maps of Saccharomyces cerevisiae. Nature 1997, 387, 67-73.
18. Dubchak, I.; Muchnik, I.; Holbrook, S. R.; Kim, S. H. Prediction of protein folding class using global description of amino acid sequence. Proc. Natl. Acad. Sci. U.S.A. 1995, 92, 8700-8704.
19. Dubchak, I.; Muchnik, I.; Mayor, C.; Dralyuk, I.; Kim, S. H. Recognition of a protein fold in the context of the Structural Classification of Proteins (SCOP) classification. Proteins 1999, 35, 401-407.
20. Cheng, J.; Randall, A. Z.; Sweredoski, M. J.; Baldi, P. SCRATCH: a protein structure and structural feature prediction server. Nucleic Acids Res. 2005, 33, W72-W76. (Pubitemid 44529882)
21. Frishman, D.; Argos, P. Seventy-five percent accuracy in protein secondary structure prediction. Proteins 1997, 27 (3), 329-335. (Pubitemid 27149285)
22. Shi, C.; Kaminskyj, S.; Caldwell, S.; Loewen, M. C. A role for a complex between activated G protein-coupled receptors in yeast cellular mating. Proc. Natl. Acad. Sci. U.S.A. 2007, 104 (13), 5395-5400.
23. Ortiz, J.; Stemmann, O.; Rank, S.; Lechner, J. A putative protein complex consisting of Ctf19, Mcm21, and Okp1 represents a missing link in the budding yeast kinetochore. Genes Dev. 1999, 13 (9), 1140-1155. (Pubitemid 29233145)
24. Kraynack, B. A.; Chan, A.; Rosenthal, E.; Essid, M.; Umansky, B.; Waters, M. G.; Schmitt, H. D. Dsl1p, Tip20p, and the novel Dsl3(Sec39) protein are required for the stability of the Q/t-SNARE complex at the endoplasmic reticulum in yeast. Mol. Biol. Cell 2005, 16 (9), 3963-3977.
25. Chou, K. C.; Cai, Y. D. Predicting Protein-Protein Interactions from Sequences in a Hybridization Space. J. Proteome Res. 2006, 5, 316-322. (Pubitemid 43222299)
26. Ashburner, M. Gene Ontology: tool for the unification of biology. Nat. Genet. 2000, 25, 25-29.
27. Chou, J. J.; Li, H.; Salvessen, G. S.; Yuan, J.; Wagner, G. Solution structure of BID, an intracellular amplifier of apoptotic signaling. Cell 1999, 96, 615-624. (Pubitemid 29122804)
28. Oxenoid, K.; Chou, J. J. The structure of phospholamban pentamer reveals a channel-like architecture in membranes. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 10870-10875.
29. Camon, E.; Magrane, M.; Barrell, D.; Binns, D.; Fleischmann, W.; Kersey, P.; Mulder, N.; Oinn, T.; Maslen, J.; Cox, A.; Apweiler, R. The gene ontology annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro. Genome Res. 2003, 13, 662-667 (Pubitemid 36511925)
30. Peng, H.; Long, F.; Ding, C. Feature selection based on mutual information: criteria of maxdependency, max-relevance, and min-redundancy. IEEE Trans. Pattern Anal. Mach. Intell. 2005, 27, 1226-1238. (Pubitemid 41245053)
31. Salzberg, S.; Cost, S. Predicting protein secondary structure with a nearest-neighbor algorithm. J. Mol. Biol. 1992, 227, 371-374.
32. Cai, Y. D.; Qian, Z. L.; Lu, L.; Feng, K. Y.; Meng, X.; Niu, B.; Zhao, G. D.; Lu, W. C. Prediction of compounds' biological function (metabolic pathways) based on functional group composition. Mol. Diversity 2008, 12, 131-137.
33. Qian, Z. L.; Lu, L. L.; Liu, X. J.; Cai, Y. D.; Li, Y. X. An approach to predict transcription factor DNA binding site specificity based upon gene and transcription factor functional categorization. Bioinformatics 2007, 23, 2449-2454.
34. Salamov, A. A.; Solovyev, V. V. Prediction of Protein Secondary Structure by Combining Nearest-neighbor Algorithms and Multiple Sequence Alignments. J. Mol. Biol. 1995, 247, 11-15.
35. Yi, T. M.; LANDER, E. S. Protein secondary structure prediction using nearest-neighbor methods. J. Mol. Biol. 1993, 232, 1117-1129. (Pubitemid 23276425)
36. Kim, S. Protein β-turn prediction using nearest-neighbor method. Bioinformatics 2004, 20, 40-44. (Pubitemid 38088338)
37. Chou, K. C.; Zhang, C. T. Prediction of protein structural classes. Crit. Rev. Biochem. Mol. Biol. 1995, 30 (4), 275-349.