메뉴 건너뛰기




Volumn 7, Issue 5, 2004, Pages 535-545

Analyzing protein function on a genomic scale: The importance of gold-standard positives and negatives for network prediction

Author keywords

[No Author keywords available]

Indexed keywords

DNA; MESSENGER RNA;

EID: 4644306020     PISSN: 13695274     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mib.2004.08.012     Document Type: Review
Times cited : (146)

References (56)
  • 1
    • 0036649020 scopus 로고    scopus 로고
    • Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters
    • L.F. Wu, T.R. Hughes, A.P. Davierwala, M.D. Robinson, R. Stoughton, and S.J. Altschuler Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters Nat Genet 31 2002 255 265
    • (2002) Nat Genet , vol.31 , pp. 255-265
    • Wu, L.F.1    Hughes, T.R.2    Davierwala, A.P.3    Robinson, M.D.4    Stoughton, R.5    Altschuler, S.J.6
  • 16
    • 0038492417 scopus 로고    scopus 로고
    • A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae)
    • O.G. Troyanskaya, K. Dolinski, A.B. Owen, R.B. Altman, and D. Botstein A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae) Proc Natl Acad Sci USA 100 2003 8348 8353
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 8348-8353
    • Troyanskaya, O.G.1    Dolinski, K.2    Owen, A.B.3    Altman, R.B.4    Botstein, D.5
  • 17
    • 0037756723 scopus 로고    scopus 로고
    • Functional genomics and proteomics: Charting a multidimensional map of the yeast cell
    • G.D. Bader, A. Heilbut, B. Andrews, M. Tyers, T. Hughes, and C. Boone Functional genomics and proteomics: charting a multidimensional map of the yeast cell Trends Cell Biol 13 2003 344 356
    • (2003) Trends Cell Biol , vol.13 , pp. 344-356
    • Bader, G.D.1    Heilbut, A.2    Andrews, B.3    Tyers, M.4    Hughes, T.5    Boone, C.6
  • 20
    • 0037161731 scopus 로고    scopus 로고
    • Comparative assessment of large-scale data sets of protein-protein interactions
    • 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
    • (2002) Nature , vol.417 , pp. 399-403
    • Von Mering, C.1    Krause, R.2    Snel, B.3    Cornell, M.4    Oliver, S.G.5    Fields, S.6    Bork, P.7
  • 21
    • 0036805329 scopus 로고    scopus 로고
    • Bridging structural biology and genomics: Assessing protein interaction data with known complexes
    • A.M. Edwards, B. Kus, R. Jansen, D. Greenbaum, J. Greenblatt, and M. Gerstein Bridging structural biology and genomics: assessing protein interaction data with known complexes Trends Genet 18 2002 529 536
    • (2002) Trends Genet , vol.18 , pp. 529-536
    • Edwards, A.M.1    Kus, B.2    Jansen, R.3    Greenbaum, D.4    Greenblatt, J.5    Gerstein, M.6
  • 22
    • 0036580169 scopus 로고    scopus 로고
    • Protein interactions: Two methods for assessment of the reliability of high throughput observations
    • 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 Proteomics 1 2002 349 356
    • (2002) Mol Cell Proteomics , vol.1 , pp. 349-356
    • Deane, C.M.1    Salwinski, L.2    Xenarios, I.3    Eisenberg, D.4
  • 23
    • 0037482108 scopus 로고    scopus 로고
    • Assessment of the reliability of protein-protein interactions and protein function prediction
    • M. Deng, F. Sun, and T. Chen Assessment of the reliability of protein-protein interactions and protein function prediction Pac Symp Biocomput 2003 140 151
    • (2003) Pac Symp Biocomput , pp. 140-151
    • Deng, M.1    Sun, F.2    Chen, T.3
  • 27
    • 0036852181 scopus 로고    scopus 로고
    • Systematic learning of gene functional classes from DNA array expression data by using multilayer perceptrons
    • A. Mateos, J. Dopazo, R. Jansen, Y. Tu, M. Gerstein, and G. Stolovitzky Systematic learning of gene functional classes from DNA array expression data by using multilayer perceptrons Genome Res 12 2002 1703 1715 This paper discusses various problems that arise for machine-learning algorithms from the fuzzy concept of protein 'function', including the difficulty of defining class boundaries and sharing and intermingling between classes.
    • (2002) Genome Res , vol.12 , pp. 1703-1715
    • Mateos, A.1    Dopazo, J.2    Jansen, R.3    Tu, Y.4    Gerstein, M.5    Stolovitzky, G.6
  • 29
    • 0141993704 scopus 로고    scopus 로고
    • A gene-coexpression network for global discovery of conserved genetic modules
    • J.M. Stuart, E. Segal, D. Koller, and S.K. Kim A gene-coexpression network for global discovery of conserved genetic modules Science 302 2003 249 255
    • (2003) Science , vol.302 , pp. 249-255
    • Stuart, J.M.1    Segal, E.2    Koller, D.3    Kim, S.K.4
  • 30
    • 1442275858 scopus 로고    scopus 로고
    • Towards a systematic definition of protein function that scales to the genome level: Defining function in terms of interactions
    • N. Lan, R. Jansen, and M. Gerstein Towards a systematic definition of protein function that scales to the genome level: defining function in terms of interactions Proc IEEE 90 2002 1848 1858
    • (2002) Proc IEEE , vol.90 , pp. 1848-1858
    • Lan, N.1    Jansen, R.2    Gerstein, M.3
  • 34
    • 0036141992 scopus 로고    scopus 로고
    • Relating whole-genome expression data with protein-protein interactions
    • R. Jansen, D. Greenbaum, and M. Gerstein Relating whole-genome expression data with protein-protein interactions Genome Res 11 2002 37 46
    • (2002) Genome Res , vol.11 , pp. 37-46
    • Jansen, R.1    Greenbaum, D.2    Gerstein, M.3
  • 35
    • 2642566695 scopus 로고    scopus 로고
    • A probabilistic view of gene function
    • A.G. Fraser, and E.M. Marcotte A probabilistic view of gene function Nat Genet 36 2004 559 564
    • (2004) Nat Genet , vol.36 , pp. 559-564
    • Fraser, A.G.1    Marcotte, E.M.2
  • 36
    • 0037245913 scopus 로고    scopus 로고
    • BIND: The Biomolecular Interaction Network Database
    • G.D. Bader, D. Betel, and C.W. Hogue BIND: the Biomolecular Interaction Network Database Nucleic Acids Res 31 2003 248 250
    • (2003) Nucleic Acids Res , vol.31 , pp. 248-250
    • Bader, G.D.1    Betel, D.2    Hogue, C.W.3
  • 38
    • 0037264524 scopus 로고    scopus 로고
    • The GRID: The General Repository for Interaction Datasets
    • B.J. Breitkreuz, C. Stark, and M. Tyers The GRID: the General Repository for Interaction Datasets Genome Biol 4 2003 R23
    • (2003) Genome Biol , vol.4
    • Breitkreuz, B.J.1    Stark, C.2    Tyers, M.3
  • 39
    • 0037197902 scopus 로고    scopus 로고
    • Interrogating protein interaction networks through structural biology
    • P. Aloy, and R.B. Russell Interrogating protein interaction networks through structural biology Proc Natl Acad Sci USA 30 2002 5896 5901
    • (2002) Proc Natl Acad Sci USA , vol.30 , pp. 5896-5901
    • Aloy, P.1    Russell, R.B.2
  • 40
    • 0142052944 scopus 로고    scopus 로고
    • A Bayesian networks approach for predicting protein-protein interactions from genomic data
    • R. Jansen, H. Yu, D. Greenbaum, Y. Kluger, N.J. Krogan, S. Chung, A. Emili, M. Snyder, J.F. Greenblatt, and M. Gerstein A Bayesian networks approach for predicting protein-protein interactions from genomic data Science 302 2003 449 453 This study shows how well-defined, empirical reference sets of interacting and non-interacting proteins can be used to assess and combine protein-protein interaction datasets. Non-interaction datasets are used to predict interactions.
    • (2003) Science , vol.302 , pp. 449-453
    • Jansen, R.1    Yu, H.2    Greenbaum, D.3    Kluger, Y.4    Krogan, N.J.5    Chung, S.6    Emili, A.7    Snyder, M.8    Greenblatt, J.F.9    Gerstein, M.10
  • 41
    • 3042562270 scopus 로고    scopus 로고
    • Genomics, prior probability, and statistical tests of multiple hypotheses
    • K.F. Manly, D. Nettleton, and J.T. Hwang Genomics, prior probability, and statistical tests of multiple hypotheses Genome Res 14 2004 997 1001
    • (2004) Genome Res , vol.14 , pp. 997-1001
    • Manly, K.F.1    Nettleton, D.2    Hwang, J.T.3
  • 42
    • 0347473809 scopus 로고    scopus 로고
    • Gaining confidence in high-throughput protein interaction networks
    • J.S. Bader, A. Chaudhuri, J.M. Rothberg, and J. Chant Gaining confidence in high-throughput protein interaction networks Nat Biotechnol 22 2004 78 85
    • (2004) Nat Biotechnol , vol.22 , pp. 78-85
    • Bader, J.S.1    Chaudhuri, A.2    Rothberg, J.M.3    Chant, J.4
  • 43
    • 0037447257 scopus 로고    scopus 로고
    • Assessing experimentally derived interactions in a small world
    • D.S. Goldberg, and F.P. Roth Assessing experimentally derived interactions in a small world Proc Natl Acad Sci USA 100 2003 4372 4376
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 4372-4376
    • Goldberg, D.S.1    Roth, F.P.2
  • 45
    • 2942541277 scopus 로고    scopus 로고
    • Predicting co-complexed protein pairs using genomic and proteomic data integration
    • L.V. Zhang, S.L. Wong, O.D. King, and F.P. Roth Predicting co-complexed protein pairs using genomic and proteomic data integration BMC Bioinformatics 5 2004 38
    • (2004) BMC Bioinformatics , vol.5 , pp. 38
    • Zhang, L.V.1    Wong, S.L.2    King, O.D.3    Roth, F.P.4
  • 46
    • 0347824672 scopus 로고    scopus 로고
    • Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: A combined computational approach
    • M. Strong, P. Mallick, M. Pellegrini, M.J. Thompson, and D. Eisenberg Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: a combined computational approach Genome Biol 4 2003 R59
    • (2003) Genome Biol , vol.4
    • Strong, M.1    Mallick, P.2    Pellegrini, M.3    Thompson, M.J.4    Eisenberg, D.5
  • 47
    • 3042523388 scopus 로고    scopus 로고
    • Predicting protein complex membership using probabilistic network reliability
    • S. Asthana, O.D. King, F.D. Gibbons, and F.P. Roth Predicting protein complex membership using probabilistic network reliability Genome Res 14 2004 1170 1175
    • (2004) Genome Res , vol.14 , pp. 1170-1175
    • Asthana, S.1    King, O.D.2    Gibbons, F.D.3    Roth, F.P.4
  • 49
    • 0034843266 scopus 로고    scopus 로고
    • Targets of TGF beta-related signaling in Caenorhabditis elegans
    • C. Savage-Dunn Targets of TGF beta-related signaling in Caenorhabditis elegans Cytokine Growth Factor Rev 12 2001 305 312
    • (2001) Cytokine Growth Factor Rev , vol.12 , pp. 305-312
    • Savage-Dunn, C.1
  • 51
    • 0031691884 scopus 로고    scopus 로고
    • LUSH odorant-binding protein mediates chemosensory responses to alcohols in Drosophila melanogaster
    • M.S. Kim, A. Repp, and D.P. Smith LUSH odorant-binding protein mediates chemosensory responses to alcohols in Drosophila melanogaster Genetics 150 1998 711 721
    • (1998) Genetics , vol.150 , pp. 711-721
    • Kim, M.S.1    Repp, A.2    Smith, D.P.3
  • 52
    • 0032511188 scopus 로고    scopus 로고
    • Ethanol intoxication in Drosophila: Genetic and pharmacological evidence for regulation by the cAMP signaling pathway
    • M.S. Moore, J. DeZazzo, A.Y. Luk, T. Tully, C.M. Singh, and U. Heberlein Ethanol intoxication in Drosophila: Genetic and pharmacological evidence for regulation by the cAMP signaling pathway Cell 93 1998 997 1007
    • (1998) Cell , vol.93 , pp. 997-1007
    • Moore, M.S.1    Dezazzo, J.2    Luk, A.Y.3    Tully, T.4    Singh, C.M.5    Heberlein, U.6
  • 53
    • 2442477788 scopus 로고    scopus 로고
    • Genomic analysis of essentiality within protein networks
    • H. Yu, D. Greenbaum, H. Xin Lu, X. Zhu, and M. Gerstein Genomic analysis of essentiality within protein networks Trends Genet 20 2004 227 231
    • (2004) Trends Genet , vol.20 , pp. 227-231
    • Yu, H.1    Greenbaum, D.2    Xin Lu, H.3    Zhu, X.4    Gerstein, M.5
  • 55
    • 1242264487 scopus 로고    scopus 로고
    • TopNet: A tool for comparing biological sub-networks, correlating protein properties with topological statistics
    • H. Yu, X. Zhu, D. Greenbaum, J. Karro, and M. Gerstein TopNet: a tool for comparing biological sub-networks, correlating protein properties with topological statistics Nucleic Acids Res 32 2004 328 337
    • (2004) Nucleic Acids Res , vol.32 , pp. 328-337
    • Yu, H.1    Zhu, X.2    Greenbaum, D.3    Karro, J.4    Gerstein, M.5
  • 56
    • 0346156102 scopus 로고    scopus 로고
    • Detection of functional modules from protein interaction networks
    • J.B. Pereira-Leal, A.J. Enright, and C.A. Ouzounis Detection of functional modules from protein interaction networks Proteins 54 2004 49 57
    • (2004) Proteins , vol.54 , pp. 49-57
    • Pereira-Leal, J.B.1    Enright, A.J.2    Ouzounis, C.A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.