메뉴 건너뛰기




Volumn 40, Issue 3, 2010, Pages 306-317

A knowledge-driven probabilistic framework for the prediction of protein-protein interaction networks

Author keywords

"Omic" datasets; Computational systems biology; Functional genomics; Machine and statistical learning; Protein protein interaction networks

Indexed keywords

BAYESIAN NETWORKS; DATA INTEGRATION; FORECASTING;

EID: 77549085334     PISSN: 00104825     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiomed.2010.01.002     Document Type: Article
Times cited : (15)

References (37)
  • 1
    • 33644555054 scopus 로고    scopus 로고
    • Proteome survey reveals modularity of the yeast cell machinery
    • Gavin A.C., Aloy P., Grandi P., Krause R., Boesche M., Marzioch M., et al. Proteome survey reveals modularity of the yeast cell machinery. Nature 440 (2006) 631-636
    • (2006) Nature , vol.440 , pp. 631-636
    • Gavin, A.C.1    Aloy, P.2    Grandi, P.3    Krause, R.4    Boesche, M.5    Marzioch, M.6
  • 2
    • 33645453254 scopus 로고    scopus 로고
    • Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
    • Krogan N.J., Cagney G., Yu H., Zhong G., Guo X., Ignatchenko A., et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440 (2006) 637-643
    • (2006) Nature , vol.440 , pp. 637-643
    • Krogan, N.J.1    Cagney, G.2    Yu, H.3    Zhong, G.4    Guo, X.5    Ignatchenko, A.6
  • 4
    • 27144530248 scopus 로고    scopus 로고
    • Towards a proteome-scale map of the human protein-protein interaction network
    • Rual J.F., Venkatesan K., Hao T., Hirozane-Kishikawa T., Dricot A., Li N., et al. Towards a proteome-scale map of the human protein-protein interaction network. Nature 437 (2005) 1173-1178
    • (2005) Nature , vol.437 , pp. 1173-1178
    • Rual, J.F.1    Venkatesan, K.2    Hao, T.3    Hirozane-Kishikawa, T.4    Dricot, A.5    Li, N.6
  • 5
    • 25144498379 scopus 로고    scopus 로고
    • A human protein-protein interaction network: a resource for annotating the proteome
    • Stelzl U., Worm U., Lalowski M., Haenig C., Brembeck F.H., Goehler H., et al. A human protein-protein interaction network: a resource for annotating the proteome. Cell 122 (2005) 957-968
    • (2005) Cell , vol.122 , pp. 957-968
    • Stelzl, U.1    Worm, U.2    Lalowski, M.3    Haenig, C.4    Brembeck, F.H.5    Goehler, H.6
  • 6
    • 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 S., Fields S., et al. 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.5    Fields, S.6
  • 7
    • 0142052944 scopus 로고    scopus 로고
    • A Bayesian networks approach for predicting protein-protein interactions from genomic data
    • Jansen R., Yu H., Greenbaum D., Kluger Y., Krogan N.J., Chung S., et al. A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science 302 (2003) 449-453
    • (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
  • 8
    • 0038492417 scopus 로고    scopus 로고
    • A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae)
    • Troyanskaya O.G., Dolinski K., Owen A.B., Altman R.B., and Botstein D. A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). Proc. Natl. Acad. Sci. 100 (2003) 8348-8353
    • (2003) Proc. Natl. Acad. Sci. , vol.100 , pp. 8348-8353
    • Troyanskaya, O.G.1    Dolinski, K.2    Owen, A.B.3    Altman, R.B.4    Botstein, D.5
  • 9
    • 42149163727 scopus 로고    scopus 로고
    • A mixture of feature experts approach for protein-protein interaction prediction
    • Qi Y., Klein-Seetharaman J., and Bar-Joseph Z. A mixture of feature experts approach for protein-protein interaction prediction. Bioinformatics 8 Suppl. 10 (2007) S6
    • (2007) Bioinformatics , vol.8 , Issue.SUPPL. 10
    • Qi, Y.1    Klein-Seetharaman, J.2    Bar-Joseph, Z.3
  • 10
    • 22244447463 scopus 로고    scopus 로고
    • Assessing the limits of genomic data integration for predicting protein networks
    • Lu L.J., Xia Y., Paccanaro A., Yu H., and Gerstein M. Assessing the limits of genomic data integration for predicting protein networks. Genome Res. 15 (2005) 945
    • (2005) Genome Res. , vol.15 , pp. 945
    • Lu, L.J.1    Xia, Y.2    Paccanaro, A.3    Yu, H.4    Gerstein, M.5
  • 12
    • 34547693013 scopus 로고    scopus 로고
    • Probabilistic prediction and ranking of human protein-protein interactions
    • Scott M.S., and Barton G.J. Probabilistic prediction and ranking of human protein-protein interactions. Bioinformatics 8 (2007) 239
    • (2007) Bioinformatics , vol.8 , pp. 239
    • Scott, M.S.1    Barton, G.J.2
  • 13
    • 0025401005 scopus 로고
    • Research note the computational complexity of probabilistic inference using Bayesian belief networks
    • Cooper G.F. Research note the computational complexity of probabilistic inference using Bayesian belief networks. Artif. Intell. 42 (1990) 393-405
    • (1990) Artif. Intell. , vol.42 , pp. 393-405
    • Cooper, G.F.1
  • 14
    • 34247869715 scopus 로고    scopus 로고
    • Variational approximations in Bayesian model selection for finite mixture distributions
    • McGrory C.A., and Titterington D.M. Variational approximations in Bayesian model selection for finite mixture distributions. Comput. Stat. Data Anal. 51 (2007) 5352-5367
    • (2007) Comput. Stat. Data Anal. , vol.51 , pp. 5352-5367
    • McGrory, C.A.1    Titterington, D.M.2
  • 15
    • 0141920354 scopus 로고    scopus 로고
    • Comparing protein abundance and mRNA expression levels on a genomic scale
    • Greenbaum D., Colangelo C., Williams K., and Gerstein M. Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol. 4 (2003) 117
    • (2003) Genome Biol. , vol.4 , pp. 117
    • Greenbaum, D.1    Colangelo, C.2    Williams, K.3    Gerstein, M.4
  • 17
    • 77549083535 scopus 로고    scopus 로고
    • Reassessing the genomic data integration limits for the prediction of protein-protein interactions in Saccharomyces cerevisiae
    • Browne F., Wang H., Zheng H., and Azuaje F. Reassessing the genomic data integration limits for the prediction of protein-protein interactions in Saccharomyces cerevisiae. CICBC 2008 5 (2008) 28-35
    • (2008) CICBC 2008 , vol.5 , pp. 28-35
    • Browne, F.1    Wang, H.2    Zheng, H.3    Azuaje, F.4
  • 18
    • 33645821454 scopus 로고    scopus 로고
    • Assessing semantic similarity measures for the characterization of human regulatory pathways
    • Guo X., Liu R., Shriver C.D., Hu H., and Liebman M.N. Assessing semantic similarity measures for the characterization of human regulatory pathways. Bioinformatics 22 (2006) 967-973
    • (2006) Bioinformatics , vol.22 , pp. 967-973
    • Guo, X.1    Liu, R.2    Shriver, C.D.3    Hu, H.4    Liebman, M.N.5
  • 19
    • 33947328242 scopus 로고    scopus 로고
    • Choosing negative examples for the prediction of protein-protein interactions
    • Ben-Hur A., and Noble S. Choosing negative examples for the prediction of protein-protein interactions. BMC Bioinformatics 7 (2006)
    • (2006) BMC Bioinformatics , vol.7
    • Ben-Hur, A.1    Noble, S.2
  • 21
    • 33646018046 scopus 로고    scopus 로고
    • Evaluation of different biological data and computational classification methods for use in protein interaction prediction
    • Qi Y., Bar-Joseph Z., and Klein-Seetharaman J. Evaluation of different biological data and computational classification methods for use in protein interaction prediction. Proteins: Struct. Funct. Bioinformatics 63 (2006) 490-500
    • (2006) Proteins: Struct. Funct. Bioinformatics , vol.63 , pp. 490-500
    • Qi, Y.1    Bar-Joseph, Z.2    Klein-Seetharaman, J.3
  • 22
    • 18744376914 scopus 로고    scopus 로고
    • Online predicted human interaction database
    • Brown K.R., and Jurisica I. Online predicted human interaction database. Bioinformatics 21 (2005) 2076-2082
    • (2005) Bioinformatics , vol.21 , pp. 2076-2082
    • Brown, K.R.1    Jurisica, I.2
  • 24
    • 4644306020 scopus 로고    scopus 로고
    • Analyzing protein function on a genomic scale: the importance of gold-standard positives and negatives for network prediction
    • Jansen R., and Gerstein M. Analyzing protein function on a genomic scale: the importance of gold-standard positives and negatives for network prediction. Curr. Opin. Microbiol. 7 (2004) 535-545
    • (2004) Curr. Opin. Microbiol. , vol.7 , pp. 535-545
    • Jansen, R.1    Gerstein, M.2
  • 25
    • 39649083998 scopus 로고    scopus 로고
    • Integration of genomic data for inferring protein complexes from global protein-protein interaction networks
    • Zheng H., Wang H., and Glass D. Integration of genomic data for inferring protein complexes from global protein-protein interaction networks. IEEE Trans. Syst. Man Cybern. Part B: Cybern. 38 (2008) 5-16
    • (2008) IEEE Trans. Syst. Man Cybern. Part B: Cybern. , vol.38 , pp. 5-16
    • Zheng, H.1    Wang, H.2    Glass, D.3
  • 27
    • 44649191771 scopus 로고    scopus 로고
    • A decomposition algorithm for learning Bayesian network structures from data
    • Zeng Y., and Hernandez J.C. A decomposition algorithm for learning Bayesian network structures from data. Lect. Notes Comput. Sci. 5012 (2008) 441
    • (2008) Lect. Notes Comput. Sci. , vol.5012 , pp. 441
    • Zeng, Y.1    Hernandez, J.C.2
  • 28
    • 48249103910 scopus 로고    scopus 로고
    • The effects of protein interactions, gene essentiality and regulatory regions on expression variation
    • Zhou L., Ma X., and Sun F. The effects of protein interactions, gene essentiality and regulatory regions on expression variation. Syst. Biol. 2 (2008) 54
    • (2008) Syst. Biol. , vol.2 , pp. 54
    • Zhou, L.1    Ma, X.2    Sun, F.3
  • 29
    • 38049003768 scopus 로고    scopus 로고
    • Bayesian network structure ensemble learning
    • Liu F., Tian F., and Zhu Q. Bayesian network structure ensemble learning. Lect. Notes Comput. Sci. 4632 (2007) 454
    • (2007) Lect. Notes Comput. Sci. , vol.4632 , pp. 454
    • Liu, F.1    Tian, F.2    Zhu, Q.3
  • 31
    • 0035999672 scopus 로고    scopus 로고
    • Analysis of mRNA expression and protein abundance data: an approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts
    • Greenbaum D., Jansen R., and Gerstein M. Analysis of mRNA expression and protein abundance data: an approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts. Bioinformatics 18 (2002) 585-596
    • (2002) Bioinformatics , vol.18 , pp. 585-596
    • Greenbaum, D.1    Jansen, R.2    Gerstein, M.3
  • 35
    • 10744224197 scopus 로고    scopus 로고
    • Development of human protein reference database as an initial platform for approaching systems biology in humans
    • Peri S., Navarro J.D., Amanchy R., Kristiansen T.Z., Jonnalagadda C.K., Surendranath V., et al. Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res. 13 (2003) 2363
    • (2003) Genome Res. , vol.13 , pp. 2363
    • Peri, S.1    Navarro, J.D.2    Amanchy, R.3    Kristiansen, T.Z.4    Jonnalagadda, C.K.5    Surendranath, V.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.