메뉴 건너뛰기




Volumn 28, Issue 20, 2012, Pages 2662-2670

FacPad: Bayesian sparse factor modeling for the inference of pathways responsive to drug treatment

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

EID: 84870461533     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts502     Document Type: Article
Times cited : (22)

References (40)
  • 1
    • 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
  • 2
    • 0031722641 scopus 로고    scopus 로고
    • Mometasone furoate decreases adhesion molecule expression in psoriasis
    • Berti, E. et al. (1998) Mometasone furoate decreases adhesion molecule expression in psoriasis. Eur. J. Dermatol, 8, 421-426.
    • (1998) Eur. J. Dermatol , vol.8 , pp. 421-426
    • Berti, E.1
  • 3
    • 55149116287 scopus 로고    scopus 로고
    • Quality assessment for short oligonucleotide micro-array data
    • Brettschneider, J. et al. (2008) Quality assessment for short oligonucleotide micro-array data. Technometrics, 50, 241-264.
    • (2008) Technometrics , vol.50 , pp. 241-264
    • Brettschneider, J.1
  • 4
    • 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
  • 5
    • 84860490976 scopus 로고    scopus 로고
    • The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
    • Caspi, R. et al. (2012) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res., 40, D742-D753.
    • (2012) Nucleic Acids Res. , vol.40
    • Caspi, R.1
  • 6
    • 78651317084 scopus 로고    scopus 로고
    • The Comparative Toxicogenomics Database: Update 2011
    • Davis, A.P. et al. (2011) The Comparative Toxicogenomics Database: update 2011. Nucleic Acids' Res., 39, D1067-D1072.
    • (2011) Nucleic Acids Res. , vol.39
    • Davis, A.P.1
  • 8
    • 77950448057 scopus 로고    scopus 로고
    • Predicting drug-target interaction networks based on functional groups and biological features
    • He, Z. et al. (2010) Predicting drug-target interaction networks based on functional groups and biological features. PLoS One, 5, e9603.
    • (2010) PLoS One , vol.5
    • He, Z.1
  • 9
    • 58549112996 scopus 로고    scopus 로고
    • Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists
    • Huang da, W. et al. (2009a) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res., 37, 1-13.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 1-13
    • Huang Da, W.1
  • 10
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang da, W. et al. (2009b) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc, 4, 44-57.
    • (2009) Nat. Protoc , vol.4 , pp. 44-57
    • Huang Da, W.1
  • 11
    • 77952305592 scopus 로고    scopus 로고
    • Large-scale prediction of protein-protein interactions from structures
    • Hue, M. et al. (2010) Large-scale prediction of protein-protein interactions from structures. BMC Bioinformatics, 11, 144.
    • (2010) BMC Bioinformatics , vol.11 , pp. 144
    • Hue, M.1
  • 12
    • 59649109178 scopus 로고    scopus 로고
    • Identifying network of drug mode of action by gene expression profiling
    • Iorio, F. et al. (2009) Identifying network of drug mode of action by gene expression profiling. J. Comput. Biol., 16, 241-251.
    • (2009) J. Comput. Biol. , vol.16 , pp. 241-251
    • Iorio, F.1
  • 13
    • 77957044703 scopus 로고    scopus 로고
    • Discovery of drug mode of action and drug repositioning from transcriptional responses
    • Iorio, F. et al. (2010) Discovery of drug mode of action and drug repositioning from transcriptional responses. Proc. Natl. Acad. Sei. USA., 107, 14621-14626.
    • (2010) Proc. Natl. Acad. Sei. USA. , vol.107 , pp. 14621-14626
    • Iorio, F.1
  • 14
    • 78049449443 scopus 로고    scopus 로고
    • Drug-induced regulation of target expression
    • Iskar, M. et al. (2010) Drug-induced regulation of target expression. PloS Comput. Biol., 6, el000925.
    • (2010) PloS Comput. Biol. , vol.6
    • Iskar, M.1
  • 15
    • 84858983547 scopus 로고    scopus 로고
    • KEGG for integration and interpretation of large-scale molecular data sets
    • Kanehisa, M. et al. (2012) KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res., 40, D109-D114.
    • (2012) Nucleic Acids Res. , vol.40
    • Kanehisa, M.1
  • 16
    • 8844263008 scopus 로고    scopus 로고
    • Docking and scoring in virtual screening for drug discovery: Methods and applications
    • Kitchen, D.B. et al. (2004) Docking and scoring in virtual screening for drug discovery: methods and applications. Nat. Rev. Drug Discov., 3, 935-949.
    • (2004) Nat. Rev. Drug Discov. , vol.3 , pp. 935-949
    • Kitchen, D.B.1
  • 17
    • 84555188306 scopus 로고    scopus 로고
    • The KEGG databases and tools facilitating omics analysis: Latest developments involving human diseases and pharmaceuticals
    • Kotera, M. et al. (2012) The KEGG databases and tools facilitating omics analysis: latest developments involving human diseases and pharmaceuticals. Methods Mol. Biol., 802, 19-39.
    • (2012) Methods Mol. Biol. , vol.802 , pp. 19-39
    • Kotera, M.1
  • 18
    • 33845876254 scopus 로고    scopus 로고
    • The Connectivity Map: A new tool for biomedical research
    • Lamb, J. (2007) The Connectivity Map: a new tool for biomedical research. Nat. Rev. Cancer, 7, 54-60.
    • (2007) Nat. Rev. Cancer , vol.7 , pp. 54-60
    • Lamb, J.1
  • 19
    • 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
  • 20
    • 18844405941 scopus 로고    scopus 로고
    • Role of retinoid signalling in the adult brain
    • Lane, M.A. and Bailey, SJ. (2005) Role of retinoid signalling in the adult brain. Prog. Neurobiol, 75, 275-293.
    • (2005) Prog. Neurobiol , vol.75 , pp. 275-293
    • Lane, M.A.1    Bailey, S.J.2
  • 21
    • 0034702030 scopus 로고    scopus 로고
    • Decreased expression of striatal signaling genes in a mouse model of Huntington's disease
    • Luthi-Carter, R. et al. (2000) Decreased expression of striatal signaling genes in a mouse model of Huntington's disease. Hum. Mol. Genet., 9, 1259-1271.
    • (2000) Hum. Mol. Genet. , vol.9 , pp. 1259-1271
    • Luthi-Carter, R.1
  • 22
    • 84864141914 scopus 로고    scopus 로고
    • IFad: An integrative factor analysis model for drug-pathway association inference
    • Ma, H. and Zhao, H. (2012) iFad: an integrative factor analysis model for drug-pathway association inference. Bioinformatics, 28, 1911-8.
    • (2012) Bioinformatics , vol.28 , pp. 1911-1918
    • Ma, H.1    Zhao, H.2
  • 23
    • 0038054341 scopus 로고    scopus 로고
    • PGC-1 alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes
    • Mootha, V.K. et al. (2003) PGC-1 alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat. Genet., 34, 267-273.
    • (2003) Nat. Genet. , vol.34 , pp. 267-273
    • Mootha, V.K.1
  • 24
    • 67650895854 scopus 로고    scopus 로고
    • Integrating statistical predictions and experimental verifications for enhancing protein-chemical interaction predictions in virtual screening
    • Nagamine, N. et al. (2009) Integrating statistical predictions and experimental verifications for enhancing protein-chemical interaction predictions in virtual screening. PLoS Comput. Biol, 5, el000397.
    • (2009) PLoS Comput. Biol , vol.5
    • Nagamine, N.1
  • 25
    • 33747360179 scopus 로고    scopus 로고
    • Chronic administration of 13-cis-retinoic acid increases depression-related behavior in mice
    • O'Reilly, K.C. et al.
    • O'Reilly, K.C. et al. (2006) Chronic administration of 13-cis-retinoic acid increases depression-related behavior in mice. Neuropsychopharmacology, 31, 1919-1927.
    • (2006) Neuropsychopharmacology , vol.31 , pp. 1919-1927
  • 26
    • 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
  • 27
    • 74349093161 scopus 로고    scopus 로고
    • Inference algorithms and learning theory for Bayesian sparse factor analysis
    • doi:10.1088/1742-6596/197/1/012002
    • Rattray, M. et al (2009) Inference algorithms and learning theory for Bayesian sparse factor analysis. J. Phys.: Conf. Ser. 197, 012002 doi:10.1088/1742-6596/197/1/012002.
    • (2009) J. Phys.: Conf. Ser. , vol.197 , pp. 012002
    • Rattray, M.1
  • 28
    • 33645107349 scopus 로고    scopus 로고
    • Bayesian sparse hidden components analysis for transcription regulation networks
    • Sabatti, C. and James, GM. (2006) Bayesian sparse hidden components analysis for transcription regulation networks. Bioinformatics, 22, 739-746.
    • (2006) Bioinformatics , vol.22 , pp. 739-746
    • Sabatti, C.1    James, G.M.2
  • 29
    • 33749011163 scopus 로고    scopus 로고
    • The NCI60 human tumour cell line anticancer drug screen
    • Shoemaker, RH. (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
  • 30
    • 76749123852 scopus 로고    scopus 로고
    • Application of connectivity mapping in predictive toxicology based on gene-expression similarity
    • Smalley, J.L. et al (2010) Application of connectivity mapping in predictive toxicology based on gene-expression similarity. Toxicology, 268, 143-146.
    • (2010) Toxicology , vol.268 , pp. 143-146
    • Smalley, J.L.1
  • 31
    • 27344435774 scopus 로고    scopus 로고
    • Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
    • Subramanian, A. et al (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sei USA., 102, 15545-15550.
    • (2005) Proc. Natl Acad. Sei USA. , vol.102 , pp. 15545-15550
    • Subramanian, A.1
  • 32
    • 27744514095 scopus 로고    scopus 로고
    • Effects of mometasone furoate on a rat allergic rhinitis model
    • Tsumuro, T. et al (2005) Effects of mometasone furoate on a rat allergic rhinitis model. Eur. J. Pharmacol, 524, 155-158.
    • (2005) Eur. J. Pharmacol , vol.524 , pp. 155-158
    • Tsumuro, T.1
  • 33
    • 67249095008 scopus 로고    scopus 로고
    • Alignment-free prediction of a drug-target complex network based on parameters of drug connectivity and protein sequence of receptors
    • Vina, D. et al (2009) Alignment-free prediction of a drug-target complex network based on parameters of drug connectivity and protein sequence of receptors. Mol Pharm., 6, 825-835.
    • (2009) Mol Pharm. , vol.6 , pp. 825-835
    • Vina, D.1
  • 34
    • 0242295767 scopus 로고    scopus 로고
    • Bayesian factor regression models in the'Large p, Small n' paradigm
    • West, M. (2003) Bayesian factor regression models in the 'Large p, Small n' paradigm. Bayesian Stat, 7, 733-742.
    • (2003) Bayesian Stat , vol.7 , pp. 733-742
    • West, M.1
  • 35
    • 84855882587 scopus 로고    scopus 로고
    • Novel computational approaches to polypharmacology as a means to define responses to individual drugs
    • Xie, L. et al (2012) Novel computational approaches to polypharmacology as a means to define responses to individual drugs. Annu. Rev. Pharmacol Toxicol, 52, 361-379.
    • (2012) Annu. Rev. Pharmacol Toxicol , vol.52 , pp. 361-379
    • Xie, L.1
  • 36
    • 46249090791 scopus 로고    scopus 로고
    • Prediction of drug-target interaction networks from the integration of chemical and genomic spaces
    • Yamanishi, Y. et al (2008) Prediction of drug-target interaction networks from the integration of chemical and genomic spaces. Bioinformatics, 24, i232-i240.
    • (2008) Bioinformatics , vol.24
    • Yamanishi, Y.1
  • 37
    • 77954230951 scopus 로고    scopus 로고
    • Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework
    • Yamanishi, Y. et al (2010) Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework. Bioinformatics, 26, i246-i254.
    • (2010) Bioinformatics , vol.26
    • Yamanishi, Y.1
  • 38
    • 37249026328 scopus 로고    scopus 로고
    • Integrating high-content screening and ligand-target prediction to identify mechanism of action
    • Young, D.W. et al (2008) Integrating high-content screening and ligand-target prediction to identify mechanism of action. Nat. Chem. Biol, 4, 59-68.
    • (2008) Nat. Chem. Biol , vol.4 , pp. 59-68
    • Young, D.W.1
  • 39
    • 84855906454 scopus 로고    scopus 로고
    • Systems pharmacology: Network analysis to identify multiscale mechanisms of drug action
    • Zhao, S. and Iyengar, R. (2012) Systems pharmacology: network analysis to identify multiscale mechanisms of drug action. Annu. Rev. Pharmacol. Toxicol, 52, 505-521.
    • (2012) Annu. Rev. Pharmacol. Toxicol , vol.52 , pp. 505-521
    • Zhao, S.1    Iyengar, R.2
  • 40
    • 77949497025 scopus 로고    scopus 로고
    • Solving the apparent diversity-accuracy dilemma of recom-mender systems
    • Zhou, T. et al (2010) Solving the apparent diversity-accuracy dilemma of recom-mender systems. Proc. Natl. Acad. Sei. USA., 107, 4511-4515.
    • (2010) Proc. Natl. Acad. Sei. USA. , vol.107 , pp. 4511-4515
    • Zhou, T.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.