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Response to McDermott and Samudrala: Enhanced functional information from predicted protein networks

Authors :
Edward M. Marcotte
Shailesh V. Date
Source :
Trends in Biotechnology. 22:62-63
Publication Year :
2004
Publisher :
Elsevier BV, 2004.

Abstract

References 1 Gavin, A.C. et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141–147 2 Schwikowski, B. et al. (2000) A network of protein–protein interactions in yeast. Nat. Biotechnol. 18, 1257–1261 3 von Mering, C. et al. (2002) Comparative assessment of large-scale data sets of protein–protein interactions. Nature 417, 399–403 4 Date, S.V. and Marcotte, E.M. (2003) Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages. Nat. Biotechnol. 21, 1055–1062 5 Huynen, M. et al. (2000) Exploitation of gene context. Curr. Opin. Struct. Biol. 10, 366–370 6 Marcotte, E.M. (2000) Computational genetics: finding protein function by nonhomology methods. Curr. Opin. Struct. Biol. 10, 359–365 7 McDermott, J. and Samudrala, R. (2003) Bioverse: functional, structural and contextual annotation of proteins and proteomes. Nucleic Acids Res. 31, 3736–3737 8 Ito, T. et al. (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. U. S. A. 98, 4569–4574 9 Rain, J.C. et al. (2001) The protein–protein interaction map of Helicobacter pylori. Nature 409, 211–215 10 Uetz, P. et al. (2000) A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae. Nature 403, 623–627 11 Rives, A.W. and Galitski, T. (2003) Modular organization of cellular networks. Proc. Natl. Acad. Sci. U. S. A. 100, 1128–1133 12 Jeong, H. et al. (2001) Lethality and centrality in protein networks. Nature 411, 41–42 13 Wojcik, J. et al. (2002) Prediction, assessment and validation of protein interaction maps in bacteria. J. Mol. Biol. 323, 763–770 14 Matthews, L.R. et al. (2001) Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or ‘interologs’. Genome Res. 11, 2120–2126 15 Ramani, A.K. and Marcotte, E.M. (2003) Exploiting the co-evolution of interacting proteins to discover interaction specificity. J. Mol. Biol. 327, 273–284 16 Pellegrini, M. et al. (1999) Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl. Acad. Sci. U. S. A. 96, 4285–4288 17 Vazquez, A. et al. (2003) Global protein function prediction from protein–protein interaction networks. Nat. Biotechnol. 21, 697–700 18 Letovsky, S. and Kasif, S. (2003) Predicting protein function from protein–protein interaction data: a probabilistic approach. Bioinformatics 19 (Suppl. 1), I197–I204 19 The GO Consortium, (2001) Creating the gene ontology resource: design and implementation. Genome Res. 11, 1425–1433 20 Yanai, I. and DeLisi, C. (2002) The society of genes: networks of functional links between genes from comparative genomics. Genome Biol. 3, research0064.1–research0064.12.

Details

ISSN :
01677799
Volume :
22
Database :
OpenAIRE
Journal :
Trends in Biotechnology
Accession number :
edsair.doi...........461a652193c7a723c156265b6a1bbc04
Full Text :
https://doi.org/10.1016/j.tibtech.2003.11.008