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Volumn 28, Issue 14, 2012, Pages 1911-1918

Ifad: An integrative factor analysis model for drug-pathway association inference†

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; BAYES THEOREM; COMPUTER SIMULATION; DRUG DEVELOPMENT; FACTORIAL ANALYSIS; HUMAN; METHODOLOGY; STATISTICAL MODEL; TUMOR CELL LINE;

EID: 84864141914     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts285     Document Type: Article
Times cited : (26)

References (41)
  • 1
    • 78651324797 scopus 로고    scopus 로고
    • CancerResource: a comprehensive database of cancer-relevant proteins and compound interactions supported by experimental knowledge
    • Ahmed, J. et al. (2011) CancerResource: a comprehensive database of cancer-relevant proteins and compound interactions supported by experimental knowledge. Nucleic Acids Res., 39, D960-D967.
    • (2011) Nucleic Acids Res , vol.39
    • Ahmed, J.1
  • 2
    • 33644873677 scopus 로고    scopus 로고
    • Pathguide: a pathway resource list
    • Bader, G. D. et al. (2006) Pathguide: a pathway resource list. Nucleic Acids Res., 34, D504-D506.
    • (2006) Nucleic Acids Res , vol.34
    • Bader, G.D.1
  • 3
    • 70449522914 scopus 로고    scopus 로고
    • Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site
    • Boyce, S. E. et al. (2009) Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site. J. Mol. Biol., 394, 747-763.
    • (2009) J. Mol. Biol. , vol.394 , pp. 747-763
    • Boyce, S.E.1
  • 4
    • 33646541046 scopus 로고    scopus 로고
    • Integrating data on DNA copy number with gene expression levels and drug sensitivities in the NCI-60 cell line panel
    • Bussey, K. J. et al. (2006) Integrating data on DNA copy number with gene expression levels and drug sensitivities in the NCI-60 cell line panel. Mol. Cancer Ther., 5, 853-867.
    • (2006) Mol. Cancer Ther. , vol.5 , pp. 853-867
    • Bussey, K.J.1
  • 5
    • 47249146126 scopus 로고    scopus 로고
    • Drug target identification using side-effect similarity
    • Campillos, M. et al. (2008) Drug target identification using side-effect similarity. Science, 321, 263-266.
    • (2008) Science , vol.321 , pp. 263-266
    • Campillos, M.1
  • 6
    • 14544287454 scopus 로고    scopus 로고
    • Bayesian network learning with feature abstraction for genedrug dependency analysis
    • Chang, J. H. et al. (2005) Bayesian network learning with feature abstraction for genedrug dependency analysis. J. Bioinform. Comput. Biol., 3, 61-77.
    • (2005) J. Bioinform. Comput. Biol. , vol.3 , pp. 61-77
    • Chang, J.H.1
  • 7
    • 73149109513 scopus 로고    scopus 로고
    • Harnessing gene expression to identify the genetic basis of drug resistance
    • Chen, B. J. et al. (2009) Harnessing gene expression to identify the genetic basis of drug resistance. Mol. Syst. Biol., 5, 310.
    • (2009) Mol. Syst. Biol. , vol.5 , pp. 310
    • Chen, B.J.1
  • 8
    • 42149140094 scopus 로고    scopus 로고
    • Genomic profiling of 766 cancer-related genes in archived esophageal normal and carcinoma tissues
    • Chen, J. et al. (2008) Genomic profiling of 766 cancer-related genes in archived esophageal normal and carcinoma tissues. Int. J. cancer, 122, 2249-2254.
    • (2008) Int. J. cancer , vol.122 , pp. 2249-2254
    • Chen, J.1
  • 9
    • 66449133301 scopus 로고    scopus 로고
    • Computational approaches to predict drug metabolism
    • Czodrowski, P. et al. (2009) Computational approaches to predict drug metabolism. Expert Opin. Drug Metab. Toxicol., 5, 15-27.
    • (2009) Expert Opin. Drug Metab. Toxicol. , vol.5 , pp. 15-27
    • Czodrowski, P.1
  • 10
    • 58149200928 scopus 로고    scopus 로고
    • Comparative toxicogenomics database: a knowledgebase and discovery tool for chemical-gene-disease networks
    • Davis, A. P. et al. (2009) Comparative toxicogenomics database: a knowledgebase and discovery tool for chemical-gene-disease networks. Nucleic Acids Res., 37, D786-D792.
    • (2009) Nucleic Acids Res , vol.37
    • Davis, A.P.1
  • 11
    • 41549102797 scopus 로고    scopus 로고
    • Computational models for prediction of interactions with ABC-transporters
    • Ecker, G. F. et al. (2008) Computational models for prediction of interactions with ABC-transporters. Drug Discov. Today, 13, 311-317.
    • (2008) Drug Discov. Today , vol.13 , pp. 311-317
    • Ecker, G.F.1
  • 12
    • 33644845723 scopus 로고    scopus 로고
    • Computational identification of key biological modules and transcription factors in acute lung injury
    • Gharib, S. A. et al. (2006) Computational identification of key biological modules and transcription factors in acute lung injury. Am. J. Respir. Crit. Care Med., 173, 653-658.
    • (2006) Am. J. Respir. Crit. Care Med. , vol.173 , pp. 653-658
    • Gharib, S.A.1
  • 13
    • 38549137931 scopus 로고    scopus 로고
    • The pharmacogenetics and pharmacogenomics knowledge base: accentuating the knowledge
    • Hernandez-Boussard, T. et al. (2008) The pharmacogenetics and pharmacogenomics knowledge base: accentuating the knowledge. Nucleic Acids Res., 36, D913-D918.
    • (2008) Nucleic Acids Res , vol.36
    • Hernandez-Boussard, T.1
  • 15
    • 33845200848 scopus 로고    scopus 로고
    • Mutation analysis of 24 known cancer genes in the NCI-60 cell line set
    • Ikediobi, O. N. et al. (2006) Mutation analysis of 24 known cancer genes in the NCI-60 cell line set. Mol. Cancer Ther., 5, 2606-2612.
    • (2006) Mol. Cancer Ther. , vol.5 , pp. 2606-2612
    • Ikediobi, O.N.1
  • 16
    • 70349211752 scopus 로고    scopus 로고
    • Automated docking screens: a feasibility study
    • Irwin, J. J. et al. (2009) Automated docking screens: a feasibility study. J. Med. Chem., 52, 5712-5720.
    • (2009) J. Med. Chem. , vol.52 , pp. 5712-5720
    • Irwin, J.J.1
  • 17
    • 75549090213 scopus 로고    scopus 로고
    • KEGG for representation and analysis of molecular networks involving diseases and drugs
    • Kanehisa, M. et al. (2010) KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res., 38, D355-D360.
    • (2010) Nucleic Acids Res , vol.38
    • Kanehisa, M.1
  • 18
    • 70349768241 scopus 로고    scopus 로고
    • Docking and chemoinformatic screens for new ligands and targets
    • Kolb, P. et al. (2009) Docking and chemoinformatic screens for new ligands and targets. Curr. Opin. Biotechnol., 20, 429-436.
    • (2009) Curr. Opin. Biotechnol. , vol.20 , pp. 429-436
    • Kolb, P.1
  • 19
    • 38549130733 scopus 로고    scopus 로고
    • STITCH: interaction networks of chemicals and proteins
    • Kuhn, M. et al. (2008) STITCH: interaction networks of chemicals and proteins. Nucleic Acids Res., 36, D684-D688.
    • (2008) Nucleic Acids Res , vol.36
    • Kuhn, M.1
  • 20
    • 43449088832 scopus 로고    scopus 로고
    • A modular approach for integrative analysis of large-scale gene-expression and drug-response data
    • Kutalik, Z. et al. (2008) A modular approach for integrative analysis of large-scale gene-expression and drug-response data. Nat. Biotechnol., 26, 531-539.
    • (2008) Nat. Biotechnol. , vol.26 , pp. 531-539
    • Kutalik, Z.1
  • 21
    • 33749335282 scopus 로고    scopus 로고
    • The connectivity map: using gene-expression signatures to connect small molecules, genes, and disease
    • Lamb, J. et al. (2006) The connectivity map: using gene-expression signatures to connect small molecules, genes, and disease. Science, 313, 1929-1935.
    • (2006) Science , vol.313 , pp. 1929-1935
    • Lamb, J.1
  • 22
    • 80054017487 scopus 로고    scopus 로고
    • Bayesian non-negative factor analysis for reconstructing transcription factor mediated regulatory networks
    • Meng, J. et al. (2011) Bayesian non-negative factor analysis for reconstructing transcription factor mediated regulatory networks. Proteome Sci., 9 (Suppl 1), S9.
    • (2011) Proteome Sci , vol.9 , Issue.SUPPL. 1
    • Meng, J.1
  • 23
    • 66449122787 scopus 로고    scopus 로고
    • Computational toxicology: an overview of the sources of data and of modelling methods
    • Nigsch, F. et al. (2009) Computational toxicology: an overview of the sources of data and of modelling methods. Expert Opin. Drug Metab. Toxicol., 5, 1-14.
    • (2009) Expert Opin. Drug Metab. Toxicol. , vol.5 , pp. 1-14
    • Nigsch, F.1
  • 24
    • 33947409985 scopus 로고    scopus 로고
    • Factor analysis for gene regulatory networks and transcription factor activity profiles
    • Pournara, I. and Wernisch, L. (2007) Factor analysis for gene regulatory networks and transcription factor activity profiles. BMC Bioinformatics, 8, 61.
    • (2007) BMC Bioinformatics , vol.8 , pp. 61
    • Pournara, I.1    Wernisch, L.2
  • 25
    • 77649182705 scopus 로고    scopus 로고
    • Unveiling the role of network and systems biology in drug discovery
    • Pujol, A. et al. (2010) Unveiling the role of network and systems biology in drug discovery. Trends Pharmacol. Sci., 31, 115-123.
    • (2010) Trends Pharmacol. Sci. , vol.31 , pp. 115-123
    • Pujol, A.1
  • 26
    • 29144531173 scopus 로고    scopus 로고
    • The druggable genome: an update
    • Russ, A. P. and Lampel, S. (2005) The druggable genome: an update. Drug Discov. Today, 10, 1607-1610.
    • (2005) Drug Discov. Today , vol.10 , pp. 1607-1610
    • Russ, A.P.1    Lampel, S.2
  • 27
    • 64049085062 scopus 로고    scopus 로고
    • Anetwork view of disease and compound screening
    • Schadt, E. E. et al. (2009)Anetwork view of disease and compound screening. Nat. Rev. Drug Discov., 8, 286-295.
    • (2009) Nat. Rev. Drug Discov. , vol.8 , pp. 286-295
    • Schadt, E.E.1
  • 28
    • 34147115178 scopus 로고    scopus 로고
    • Transcript and protein expression profiles of the NCI-60 cancer cell panel: an integromic microarray study
    • Shankavaram, U. T. et al. (2007) Transcript and protein expression profiles of the NCI-60 cancer cell panel: an integromic microarray study. Mol. Cancer Ther., 6, 820-832.
    • (2007) Mol. Cancer Ther. , vol.6 , pp. 820-832
    • Shankavaram, U.T.1
  • 29
    • 67650687092 scopus 로고    scopus 로고
    • CellMiner: a relational database and query tool for the NCI-60 cancer cell lines
    • Shankavaram, U. T. et al. (2009) CellMiner: a relational database and query tool for the NCI-60 cancer cell lines. BMC Genomics, 10, 277.
    • (2009) BMC Genomics , vol.10 , pp. 277
    • Shankavaram, U.T.1
  • 30
    • 77949957365 scopus 로고    scopus 로고
    • Cell line-based platforms to evaluate the therapeutic efficacy of candidate anticancer agents
    • Sharma, S. V. et al. (2010) Cell line-based platforms to evaluate the therapeutic efficacy of candidate anticancer agents. Nat. Rev. Cancer, 10, 241-253.
    • (2010) Nat. Rev. Cancer , vol.10 , pp. 241-253
    • Sharma, S.V.1
  • 31
    • 84875277953 scopus 로고    scopus 로고
    • A comparison of inference in sparse factor analysis
    • September
    • Sharp, K. et al. (2010) A comparison of inference in sparse factor analysis. Submitted to the J. Mach. Learn. Res., September.
    • (2010) Submitted to the J. Mach. Learn. Res.
    • Sharp, K.1
  • 32
    • 33749011163 scopus 로고    scopus 로고
    • The NCI60 human tumour cell line anticancer drug screen
    • Shoemaker, R. H. (2006) The NCI60 human tumour cell line anticancer drug screen. Nat. Rev. Cancer, 6, 813-823.
    • (2006) Nat. Rev. Cancer , vol.6 , pp. 813-823
    • Shoemaker, R.H.1
  • 33
    • 0035845531 scopus 로고    scopus 로고
    • Chemosensitivity prediction by transcriptional profiling
    • Staunton, J. E. et al. (2001) Chemosensitivity prediction by transcriptional profiling. Proc. Natl Acad. Sci. USA, 98, 10787-10792.
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 10787-10792
    • Staunton, J.E.1
  • 34
    • 0242295767 scopus 로고    scopus 로고
    • Bayesian factor regression models in the "large p, small n" paradigm
    • Bernardo, J. M. et al. (eds), Oxford University Press, Oxford, UK
    • West, M. (2003) Bayesian factor regression models in the "large p, small n" paradigm. In Bernardo, J. M. et al. (eds) Bayesian Statistics, Oxford University Press, Oxford, UK, Vol. 7, pp. 733-742.
    • (2003) Bayesian Statistics , vol.7 , pp. 733-742
    • West, M.1
  • 35
    • 38549151817 scopus 로고    scopus 로고
    • DrugBank: a knowledgebase for drugs, drug actions and drug targets
    • Wishart, D. S. et al. (2008) DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res., 36, D901-D906.
    • (2008) Nucleic Acids Res , vol.36
    • Wishart, D.S.1
  • 36
    • 75149140181 scopus 로고    scopus 로고
    • Identifying significant genetic regulatory networks in the prostate cancer from microarray data based on transcription factor analysis and conditional independency
    • Yeh, H. Y. et al. (2009) Identifying significant genetic regulatory networks in the prostate cancer from microarray data based on transcription factor analysis and conditional independency. BMC Med Genomics, 2, 70.
    • (2009) BMC Med Genomics , vol.2 , pp. 70
    • Yeh, H.Y.1
  • 37
    • 33645396484 scopus 로고    scopus 로고
    • Functional classification of drugs by properties of their pairwise interactions
    • Yeh, P. et al. (2006) Functional classification of drugs by properties of their pairwise interactions. Nat. Genet., 38, 489-494.
    • (2006) Nat. Genet. , vol.38 , pp. 489-494
    • Yeh, P.1
  • 38
    • 35148838537 scopus 로고    scopus 로고
    • Drug-target network
    • Yildirim, M. A. et al. (2007) Drug-target network. Nat. Biotechnol., 25, 1119-1126.
    • (2007) Nat. Biotechnol. , vol.25 , pp. 1119-1126
    • Yildirim, M.A.1
  • 39
    • 27744472292 scopus 로고    scopus 로고
    • Inference of transcriptional regulatory network by two-stage constrained space factor analysis
    • Yu, T. and Li, K. C. (2005) Inference of transcriptional regulatory network by two-stage constrained space factor analysis. Bioinformatics, 21, 4033-4038.
    • (2005) Bioinformatics , vol.21 , pp. 4033-4038
    • Yu, T.1    Li, K.C.2
  • 40
    • 15244353539 scopus 로고    scopus 로고
    • Side-chain flexibility in protein-ligand binding: the minimal rotation hypothesis
    • Zavodszky, M. I. and Kuhn, L. A. (2005) Side-chain flexibility in protein-ligand binding: the minimal rotation hypothesis. Protein Sci., 14, 1104-1114.
    • (2005) Protein Sci , vol.14 , pp. 1104-1114
    • Zavodszky, M.I.1    Kuhn, L.A.2
  • 41
    • 84859267371 scopus 로고    scopus 로고
    • Therapeutic target database update. 2012: a resource for facilitating target-oriented drug discovery
    • Zhu, F. et al. (2011) Therapeutic target database update 2012: a resource for facilitating target-oriented drug discovery. Nucleic Acids Res., 40, D1128-D1136.
    • (2011) Nucleic Acids Res. , vol.40
    • Zhu, F.1


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