메뉴 건너뛰기




Volumn 5, Issue , 2004, Pages

Predicting co-complexed protein pairs using genomic and proteomic data integration

Author keywords

Data integration; Decision tree; Machine learning; Protein complex; Protein protein interaction

Indexed keywords

AFFINITY PURIFICATION; EXPERIMENTAL VALIDATIONS; HIGH-THROUGHPUT METHOD; PHYSICAL INTERACTIONS; PROBABILISTIC DECISION TREES; PROTEIN COMPLEXES; PROTEIN-PROTEIN INTERACTIONS; SUPERVISED MACHINE LEARNING;

EID: 2942541277     PISSN: 14712105     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2105-5-38     Document Type: Article
Times cited : (155)

References (45)
  • 1
    • 0035895513 scopus 로고    scopus 로고
    • Gene number. What if there are only 30,000 human genes?
    • Claverie JM: Gene number. What if there are only 30,000 human genes? Science 2001, 291(5507):1255-1257.
    • (2001) Science , vol.291 , Issue.5507 , pp. 1255-1257
    • Claverie, J.M.1
  • 4
    • 0033974688 scopus 로고    scopus 로고
    • Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins
    • Ito T, Tashiro K, Muta S, Ozawa R, Chiba T, Nishizawa M, Yamamoto K, Kuhara S, Sakaki Y: Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proc Natl Acad Sci U S A 2000, 97(3):1143-1147.
    • (2000) Proc. Natl. Acad. Sci. U. S. A. , vol.97 , Issue.3 , pp. 1143-1147
    • Ito, T.1    Tashiro, K.2    Muta, S.3    Ozawa, R.4    Chiba, T.5    Nishizawa, M.6    Yamamoto, K.7    Kuhara, S.8    Sakaki, Y.9
  • 5
    • 0037161731 scopus 로고    scopus 로고
    • Comparative assessment of large-scale data sets of protein-protein interactions
    • von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P: Comparative assessment of large-scale data sets of protein-protein interactions. Nature 2002, 417(6887):399-403.
    • (2002) Nature , vol.417 , Issue.6887 , 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
  • 8
    • 0036141992 scopus 로고    scopus 로고
    • Relating whole-genome expression data with protein-protein interactions
    • Jansen R, Greenbaum D, Gerstein M: Relating whole-genome expression data with protein-protein interactions. Genome Res 2002, 12(1):37-46.
    • (2002) Genome Res. , vol.12 , Issue.1 , pp. 37-46
    • Jansen, R.1    Greenbaum, D.2    Gerstein, M.3
  • 9
    • 0035733690 scopus 로고    scopus 로고
    • Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae
    • Ge H, Liu Z, Church GM, Vidal M: Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nat Genet 2001, 29(4):482-486.
    • (2001) Nat. Genet. , vol.29 , Issue.4 , pp. 482-486
    • Ge, H.1    Liu, Z.2    Church, G.M.3    Vidal, M.4
  • 10
    • 0036580169 scopus 로고    scopus 로고
    • Protein interactions: Two methods for assessment of the reliability of high throughput observations
    • Deane CM, Salwinski L, Xenarios I, Eisenberg D: Protein interactions: two methods for assessment of the reliability of high throughput observations. Mol Cell Proteomics 2002, 1(5):349-356.
    • (2002) Mol. Cell Proteomics , vol.1 , Issue.5 , pp. 349-356
    • Deane, C.M.1    Salwinski, L.2    Xenarios, I.3    Eisenberg, D.4
  • 11
    • 0036279153 scopus 로고    scopus 로고
    • Protein interaction verification and functional annotation by integrated analysis of genome-scale data
    • Kemmeren P, van Berkum NL, Vilo J, Bijma T, Donders R, Brazma A, Holstege FC: Protein interaction verification and functional annotation by integrated analysis of genome-scale data. Mol Cell 2002, 9(5):1133-1143.
    • (2002) Mol. Cell , vol.9 , Issue.5 , pp. 1133-1143
    • Kemmeren, P.1    van Berkum, N.L.2    Vilo, J.3    Bijma, T.4    Donders, R.5    Brazma, A.6    Holstege, F.C.7
  • 12
    • 0035445792 scopus 로고    scopus 로고
    • A relationship between gene expression and protein interactions on the proteome scale: Analysis of the bacteriophage T7 and the yeast Saccharomyces cerevisiae
    • Grigoriev A: A relationship between gene expression and protein interactions on the proteome scale: analysis of the bacteriophage T7 and the yeast Saccharomyces cerevisiae. Nucleic Acids Res 2001, 29(17):3513-3519.
    • (2001) Nucleic Acids Res. , vol.29 , Issue.17 , pp. 3513-3519
    • Grigoriev, A.1
  • 13
    • 0141561891 scopus 로고    scopus 로고
    • Integrating 'omic' information: A bridge between genomics and systems biology
    • Ge H, Walhout AJ, Vidal M: Integrating 'omic' information: a bridge between genomics and systems biology. Trends Genet 2003, 19(10):551-560.
    • (2003) Trends Genet. , vol.19 , Issue.10 , pp. 551-560
    • Ge, H.1    Walhout, A.J.2    Vidal, M.3
  • 14
    • 0033669189 scopus 로고    scopus 로고
    • A network of protein-protein interactions in yeast
    • Schwikowski B, Uetz P, Fields S: A network of protein-protein interactions in yeast. Nat Biotechnol 2000, 18(12):1257-1261.
    • (2000) Nat. Biotechnol. , vol.18 , Issue.12 , pp. 1257-1261
    • Schwikowski, B.1    Uetz, P.2    Fields, S.3
  • 17
    • 0033618555 scopus 로고    scopus 로고
    • Detecting protein function and protein-protein interactions from genome sequences
    • Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO, Eisenberg D: Detecting protein function and protein-protein interactions from genome sequences. Science 1999, 285(5428):751-753.
    • (1999) Science , vol.285 , Issue.5428 , pp. 751-753
    • Marcotte, E.M.1    Pellegrini, M.2    Ng, H.L.3    Rice, D.W.4    Yeates, T.O.5    Eisenberg, D.6
  • 19
    • 0036100116 scopus 로고    scopus 로고
    • Learning gene functional classifications from multiple data types
    • Pavlidis P, Weston J, Cai J, Noble WS: Learning gene functional classifications from multiple data types. J Comput Biol 2002, 9(2):401-411.
    • (2002) J. Comput. Biol. , vol.9 , Issue.2 , pp. 401-411
    • Pavlidis, P.1    Weston, J.2    Cai, J.3    Noble, W.S.4
  • 21
    • 0038492417 scopus 로고    scopus 로고
    • A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae)
    • Troyanskaya OG, Dolinski K, Owen AB, Altman RB, Botstein D: A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). Proc Natl Acad Sci U S A 2003, 100(14):8348-8353.
    • (2003) Proc. Natl. Acad. Sci. U. S. A. , vol.100 , Issue.14 , pp. 8348-8353
    • Troyanskaya, O.G.1    Dolinski, K.2    Owen, A.B.3    Altman, R.B.4    Botstein, D.5
  • 24
    • 84874659446 scopus 로고    scopus 로고
    • MIPS complex catalogue
    • MIPS complex catalogue [http://mips.gsf.de/proj/yeast/catalogues/complexes/index.html]
  • 28
    • 0028293432 scopus 로고
    • Suppression of yeast RNA polymerase III mutations by FHL1, a gene coding for a fork head protein involved in rRNA processing
    • Hermann-Le Denmat S, Werner M, Sentenac A, Thuriaux P: Suppression of yeast RNA polymerase III mutations by FHL1, a gene coding for a fork head protein involved in rRNA processing. Mol Cell Biol 1994, 14(5):2905-2913.
    • (1994) Mol. Cell Biol. , vol.14 , Issue.5 , pp. 2905-2913
    • Hermann-Le Denmat, S.1    Werner, M.2    Sentenac, A.3    Thuriaux, P.4
  • 30
    • 0036789265 scopus 로고    scopus 로고
    • Analyzing yeast protein-protein interaction data obtained from different sources
    • Bader GD, Hogue CW: Analyzing yeast protein-protein interaction data obtained from different sources. Nat Biotechnol 2002, 20(10):991-997.
    • (2002) Nat. Biotechnol. , vol.20 , Issue.10 , pp. 991-997
    • Bader, G.D.1    Hogue, C.W.2
  • 31
    • 2942552459 scopus 로고    scopus 로고
    • An automated method for finding molecular complexes in large protein interaction networks
    • Bader GD, Hogue CW: An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 2003, 4(1):2.
    • (2003) BMC Bioinformatics , vol.4 , Issue.1 , pp. 2
    • Bader, G.D.1    Hogue, C.W.2
  • 32
    • 0032563246 scopus 로고    scopus 로고
    • Crystallographic analysis of the recognition of a nuclear localization signal by the nuclear import factor karyopherin alpha
    • Conti E, Uy M, Leighton L, Blobel G, Kuriyan J: Crystallographic analysis of the recognition of a nuclear localization signal by the nuclear import factor karyopherin alpha. Cell 1998, 94(2):193-204.
    • (1998) Cell , vol.94 , Issue.2 , pp. 193-204
    • Conti, E.1    Uy, M.2    Leighton, L.3    Blobel, G.4    Kuriyan, J.5
  • 33
    • 0030771087 scopus 로고    scopus 로고
    • Small nucleolar RNAs direct site-specific synthesis of pseudouridine in ribosomal RNA
    • Ni J, Tien AL, Fournier MJ: Small nucleolar RNAs direct site-specific synthesis of pseudouridine in ribosomal RNA. Cell 1997, 89(4):565-573.
    • (1997) Cell , vol.89 , Issue.4 , pp. 565-573
    • Ni, J.1    Tien, A.L.2    Fournier, M.J.3
  • 34
    • 0028318459 scopus 로고
    • SRD1, a S. cerevisiae gene affecting prerRNA processing contains a C2/C2 zinc finger motif
    • Hess SM, Stanford DR, Hopper AK: SRD1, a S. cerevisiae gene affecting prerRNA processing contains a C2/C2 zinc finger motif. Nucleic Acids Res 1994, 22(7):1265-1271.
    • (1994) Nucleic Acids Res. , vol.22 , Issue.7 , pp. 1265-1271
    • Hess, S.M.1    Stanford, D.R.2    Hopper, A.K.3
  • 35
    • 0142241336 scopus 로고    scopus 로고
    • Greedily building protein networks with confidence
    • Bader JS: Greedily building protein networks with confidence. Bioinformatics 2003, 19(15):1869-1874.
    • (2003) Bioinformatics , vol.19 , Issue.15 , pp. 1869-1874
    • Bader, J.S.1
  • 36
    • 84874662095 scopus 로고    scopus 로고
    • Predicting protein complex membership using probabilistic network reliability
    • in press
    • Asthana S, King OD, Roth FP: Predicting protein complex membership using probabilistic network reliability. Genome Res in press.
    • Genome Res.
    • Asthana, S.1    King, O.D.2    Roth, F.P.3
  • 37
    • 0037059506 scopus 로고    scopus 로고
    • Proteomics. Integrating interactomes
    • Gerstein M, Lan N, Jansen R: Proteomics. Integrating interactomes. Science 2002, 295(5553):284-287.
    • (2002) Science , vol.295 , Issue.5553 , pp. 284-287
    • Gerstein, M.1    Lan, N.2    Jansen, R.3
  • 39
    • 2942590700 scopus 로고    scopus 로고
    • Predicting the effects of gene deletion
    • Vogel DS, Axelrod RC: Predicting the effects of gene deletion. SIGKDD Explorations 2002, 4(2):101.
    • (2002) SIGKDD Explorations , vol.4 , Issue.2 , pp. 101
    • Vogel, D.S.1    Axelrod, R.C.2
  • 40
    • 0003500248 scopus 로고
    • C4.5 : Programs for machine learning
    • San Mateo, Calif.: Morgan Kaufmann Publishers
    • Quinlan JR: C4.5 : programs for machine learning. San Mateo, Calif.: Morgan Kaufmann Publishers; 1993.
    • (1993)
    • Quinlan, J.R.1
  • 41
    • 0003802343 scopus 로고
    • Classification and regression trees
    • Belmont, Calif.: Wadsworth International Group
    • Breiman L, Friedman JH, Olshen RA, Stone CJ: Classification and regression trees. Belmont, Calif.: Wadsworth International Group; 1984.
    • (1984)
    • Breiman, L.1    Friedman, J.H.2    Olshen, R.A.3    Stone, C.J.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.