Faster and more accurate global protein function assignment from protein interaction networks using the MFGO algorithm

FEBS Letters

Volumn 580, Issue 7, 2006, Pages 1891-1896

  Sun, Shiwei ^a   Zhao, Yi ^a   Jiao, Yishan ^a   Yin, Yifei ^a   Cai, Lun ^a   Zhang, Yong ^b   Lu, Hongchao ^a   Chen, Runsheng ^a,b   Bu, Dongbo ^a  

^a INSTITUTE OF COMPUTING TECHNOLOGY   (China)

^b INSTITUTE OF BIOPHYSICS   (China)

Author keywords

Function prediction; Global optimization; Protein interaction network

Indexed keywords

ALGORITHM; ARTICLE; CALCULATION; CONTROLLED STUDY; NONHUMAN; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN STRUCTURE; VALIDATION PROCESS;

ALGORITHMS; MODELS, MOLECULAR; PROTEINS; SACCHAROMYCES CEREVISIAE PROTEINS; TIME FACTORS;

EID: 33644895409     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.febslet.2006.02.053     Document Type: Article

References (14)

1. G.D. Bader, D. Betel, and C.W. Hogue BIND: the biomolecular interaction network database Nucleic Acids Res 31 2003 248 250
2. C. Brun, F. Chevenet, D. Martin, J. Wojcik, A. Guenoche, and B. Jacq Functional classification of proteins for the prediction of cellular function from a protein-protein interaction network Genome Biol. 5 2003 R6
3. C.M. Deane, L. Salwinski, I. Xenarios, and D. Eisenberg Protein interactions: two methods for assessment of the reliability of high throughput observations Mol. Cell. Proteom. 1 2002 349 356
4. M. Deng, K. Zhang, S. Mehta, T. Chen, and F. Sun Prediction of protein function using protein-protein interaction data J. Comput. Biol. 10 2003 947 960
5. J. Espadaler, R. Aragues, N. Eswar, M.A. Marti-Renom, E. Querol, F.X. Aviles, A. Sali, and B. Oliva Detecting remotely related proteins by their interactions and sequence similarity Proc. Natl. Acad. Sci. USA 102 2005 7151 7156
6. A.C. Gavin, M. Bosche, R. Krause, P. Grandi, M. Marzioch, A. Bauer, J. Schultz, J.M. Rick, A.M. Michon, C.M. Cruciat, M. Remor, C. Hofert, M. Schelder, M. Brajenovic, H. Ruffner, A. Merino, K. Klein, M. Hudak, D. Dickson, T. Rudi, V. Gnau, A. Bauch, S. Bastuck, B. Huhse, C. Leutwein, M.A. Heurtier, R.R. Copley, A. Edelmann, E. Querfurth, V. Rybin, G. Drewes, M. Raida, T. Bouwmeester, P. Bork, B. Seraphin, B. Kuster, G. Neubauer, and G. Superti-Furga Functional organization of the yeast proteome by systematic analysis of protein complexes Nature 415 2002 141 147
7. H. Hishigaki, K. Nakai, T. Ono, A. Tanigami, and T. Takagi Assessment of prediction accuracy of protein function from protein-protein interaction data Yeast 18 2001 523 531
8. Y. Ho, A. Gruhler, A. Heilbut, G.D. Bader, L. Moore, S.L. Adams, A. Millar, P. Taylor, K. Bennett, K. Boutilier, L. Yang, C. Wolting, I. Donaldson, S. Schandorff, J. Shewnarane, M. Vo, J. Taggart, M. Goudreault, B. Muskat, C. Alfarano, D. Dewar, Z. Lin, K. Michalickova, A.R. Willems, H. Sassi, P.A. Nielsen, K.J. Rasmussen, J.R. Andersen, L.E. Johansen, L.H. Hansen, H. Jespersen, A. Podtelejnikov, E. Nielsen, J. Crawford, V. Poulsen, B.D. Sorensen, J. Matthiesen, R.C. Hendrickson, F. Gleeson, T. Pawson, M.F. Moran, D. Durocher, M. Mann, C.W. Hogue, D. Figeys, and M. Tyers Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry Nature 415 2002 180 183
9. K. Okada, S. Kanaya, and K. Asai Accurate extraction of functional associations between proteins based on common interaction partners and common domains Bioinformatics 21 2005 2043 2048
10. P. Pagel, S. Kovac, M. Oesterheld, B. Brauner, I. Dunger-Kaltenbach, G. Frishman, C. Montrone, P. Mark, V. Stumpflen, H.W. Mewes, A. Ruepp, and D. Frishman The MIPS mammalian protein-protein interaction database Bioinformatics 2004
11. M. Pellegrini, E.M. Marcotte, M.J. Thompson, D. Eisenberg, and T.O. Yeates Assigning protein functions by comparative genome analysis: protein phylogenetic profiles Proc. Natl. Acad. Sci. USA 96 1999 4285 4288
12. B. Schwikowski, P. Uetz, and S. Fields A network of protein-protein interactions in yeast Nat. Biotechnol. 18 2000 1257 1261
13. A. Vazquez, A. Flammini, A. Maritan, and A. Vespignani Global protein function prediction from protein-protein interaction networks Nat. Biotechnol. 21 2003 697 700
14. C. von Mering, R. Krause, B. Snel, M. Cornell, S.G. Oliver, S. Fields, and P. Bork Comparative assessment of large-scale data sets of protein-protein interactions Nature 417 2002 399 403