메뉴 건너뛰기




Volumn 9, Issue SUPPL. 1, 2011, Pages

Bayesian non-negative factor analysis for reconstructing transcription factor mediated regulatory networks

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

EID: 80054017487     PISSN: None     EISSN: 14775956     Source Type: Journal    
DOI: 10.1186/1477-5956-9-S1-S9     Document Type: Article
Times cited : (7)

References (45)
  • 1
    • 41349096445 scopus 로고    scopus 로고
    • Gene regulation by transcription factors and microRNAs
    • 10.1126/science.1151651, 18369135
    • Hobert O. Gene regulation by transcription factors and microRNAs. Science 2008, 319(5871):1785. 10.1126/science.1151651, 18369135.
    • (2008) Science , vol.319 , Issue.5871 , pp. 1785
    • Hobert, O.1
  • 3
    • 0141920354 scopus 로고    scopus 로고
    • Comparing protein abundance and mRNA expression levels on a genomic scale
    • 10.1186/gb-2003-4-9-117, 193646, 12952525
    • Greenbaum D, Colangelo C, Williams K, Gerstein M. Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol 2003, 4(9):117. 10.1186/gb-2003-4-9-117, 193646, 12952525.
    • (2003) Genome Biol , vol.4 , Issue.9 , pp. 117
    • Greenbaum, D.1    Colangelo, C.2    Williams, K.3    Gerstein, M.4
  • 4
    • 0033016717 scopus 로고    scopus 로고
    • Correlation between protein and mRNA abundance in yeast
    • 83965, 10022859
    • Gygi S, Rochon Y, Franza B, Aebersold R. Correlation between protein and mRNA abundance in yeast. Molecular and Cellular Biology 1999, 19(3):1720. 83965, 10022859.
    • (1999) Molecular and Cellular Biology , vol.19 , Issue.3 , pp. 1720
    • Gygi, S.1    Rochon, Y.2    Franza, B.3    Aebersold, R.4
  • 5
    • 33645107349 scopus 로고    scopus 로고
    • Bayesian sparse hidden components analysis for transcription regulation networks
    • 10.1093/bioinformatics/btk017, 16368767
    • Sabatti C, James G. Bayesian sparse hidden components analysis for transcription regulation networks. Bioinformatics 2006, 22(6):739. 10.1093/bioinformatics/btk017, 16368767.
    • (2006) Bioinformatics , vol.22 , Issue.6 , pp. 739
    • Sabatti, C.1    James, G.2
  • 6
    • 33751008680 scopus 로고    scopus 로고
    • Probabilistic inference of transcription factor concentrations and gene-specific regulatory activities
    • 10.1093/bioinformatics/btl473, 16966362
    • Sanguinetti G, Lawrence N, Rattray M. Probabilistic inference of transcription factor concentrations and gene-specific regulatory activities. Bioinformatics 2006, 22(22):2775. 10.1093/bioinformatics/btl473, 16966362.
    • (2006) Bioinformatics , vol.22 , Issue.22 , pp. 2775
    • Sanguinetti, G.1    Lawrence, N.2    Rattray, M.3
  • 7
    • 27744472292 scopus 로고    scopus 로고
    • Inference of transcriptional regulatory network by two-stage constrained space factor analysis
    • 10.1093/bioinformatics/bti656, 16144806
    • Yu T, Li K. Inference of transcriptional regulatory network by two-stage constrained space factor analysis. Bioinformatics 2005, 21(21):4033. 10.1093/bioinformatics/bti656, 16144806.
    • (2005) Bioinformatics , vol.21 , Issue.21 , pp. 4033
    • Yu, T.1    Li, K.2
  • 8
    • 23744491001 scopus 로고    scopus 로고
    • Predicting transcription factor activities from combined analysis of microarray and ChIP data: a partial least squares approach
    • 10.1186/1742-4682-2-23, 1182396, 15978125
    • Boulesteix A, Strimmer K. Predicting transcription factor activities from combined analysis of microarray and ChIP data: a partial least squares approach. Theoretical Biology and Medical Modelling 2005, 2:23. 10.1186/1742-4682-2-23, 1182396, 15978125.
    • (2005) Theoretical Biology and Medical Modelling , vol.2 , pp. 23
    • Boulesteix, A.1    Strimmer, K.2
  • 9
    • 0345743695 scopus 로고    scopus 로고
    • Transcriptome-based determination of multiple transcription regulator activities in Escherichia coli by using network component analysis
    • Kao K, Yang Y, Boscolo R, Sabatti C, Roychowdhury V, Liao J. Transcriptome-based determination of multiple transcription regulator activities in Escherichia coli by using network component analysis. Proceedings of the National Academy of Sciences 2004, 101(2):641.
    • (2004) Proceedings of the National Academy of Sciences , vol.101 , Issue.2 , pp. 641
    • Kao, K.1    Yang, Y.2    Boscolo, R.3    Sabatti, C.4    Roychowdhury, V.5    Liao, J.6
  • 12
    • 79952659846 scopus 로고    scopus 로고
    • Boosting Signal-to-Noise in Complex Biology: Prior Knowledge Is Power
    • 10.1016/j.cell.2011.03.007, 21414478
    • Ideker T, JHL D. Boosting Signal-to-Noise in Complex Biology: Prior Knowledge Is Power. Cell 2011, 144(6):860-863. 10.1016/j.cell.2011.03.007, 21414478.
    • (2011) Cell , vol.144 , Issue.6 , pp. 860-863
    • Ideker, T.1    JHL, D.2
  • 13
    • 60149106101 scopus 로고    scopus 로고
    • Non-negative matrix factorization of gene expression profiles: a plug-in for BRB-ArrayTools
    • 10.1093/bioinformatics/btp009, 19131367
    • Qi Q, Zhao Y, Li M, Simon R. Non-negative matrix factorization of gene expression profiles: a plug-in for BRB-ArrayTools. Bioinformatics 2009, 25(4):545. 10.1093/bioinformatics/btp009, 19131367.
    • (2009) Bioinformatics , vol.25 , Issue.4 , pp. 545
    • Qi, Q.1    Zhao, Y.2    Li, M.3    Simon, R.4
  • 14
    • 84900510076 scopus 로고    scopus 로고
    • Non-negative matrix factorization with sparseness constraints
    • Hoyer P. Non-negative matrix factorization with sparseness constraints. The Journal of Machine Learning Research 2004, 5:1469.
    • (2004) The Journal of Machine Learning Research , vol.5 , pp. 1469
    • Hoyer, P.1
  • 16
    • 62549125109 scopus 로고    scopus 로고
    • High-dimensional sparse factor modeling: Applications in gene expression genomics
    • 10.1198/016214508000000869, 3017385, 21218139
    • Carvalho C, Chang J, Lucas J, Nevins J, Wang Q, West M. High-dimensional sparse factor modeling: Applications in gene expression genomics. Journal of the American Statistical Association 2008, 103(484):1438-1456. 10.1198/016214508000000869, 3017385, 21218139.
    • (2008) Journal of the American Statistical Association , vol.103 , Issue.484 , pp. 1438-1456
    • Carvalho, C.1    Chang, J.2    Lucas, J.3    Nevins, J.4    Wang, Q.5    West, M.6
  • 17
    • 39749138525 scopus 로고    scopus 로고
    • Graphical models for visual object recognition and tracking
    • Massachusetts Institute of Technology
    • Sudderth E. Graphical models for visual object recognition and tracking. PhD thesis 2006, Massachusetts Institute of Technology.
    • (2006) PhD thesis
    • Sudderth, E.1
  • 18
    • 0001120413 scopus 로고
    • A Bayesian analysis of some nonparametric problems
    • Ferguson T. A Bayesian analysis of some nonparametric problems. The annals of statistics 1973, 1(2):209-230.
    • (1973) The annals of statistics , vol.1 , Issue.2 , pp. 209-230
    • Ferguson, T.1
  • 20
    • 0037276175 scopus 로고    scopus 로고
    • Statistical tests for differential expression in cDNA microarray experiments
    • 10.1186/gb-2003-4-4-210, 154570, 12702200
    • Cui X, Churchill G. Statistical tests for differential expression in cDNA microarray experiments. Genome Biol 2003, 4(4):210. 10.1186/gb-2003-4-4-210, 154570, 12702200.
    • (2003) Genome Biol , vol.4 , Issue.4 , pp. 210
    • Cui, X.1    Churchill, G.2
  • 21
    • 77957835537 scopus 로고    scopus 로고
    • Differential Expression and Annotation
    • Wong C. Differential Expression and Annotation. 2009,
    • (2009)
    • Wong, C.1
  • 22
    • 38549146907 scopus 로고    scopus 로고
    • DBD-taxonomically broad transcription factor predictions: new content and functionality
    • Database issue, 2238844, 18073188
    • Wilson D, Charoensawan V, Kummerfeld S, Teichmann S. DBD-taxonomically broad transcription factor predictions: new content and functionality. Nucleic Acids Research 2008, 36(Database issue):D88. 2238844, 18073188.
    • (2008) Nucleic Acids Research , vol.36
    • Wilson, D.1    Charoensawan, V.2    Kummerfeld, S.3    Teichmann, S.4
  • 28
    • 67650932694 scopus 로고    scopus 로고
    • A comparison of extrinsic clustering evaluation metrics based on formal constraints
    • Amigó E, Gonzalo J, Artiles J, Verdejo F. A comparison of extrinsic clustering evaluation metrics based on formal constraints. Information Retrieval 2009, 12(4):461-486.
    • (2009) Information Retrieval , vol.12 , Issue.4 , pp. 461-486
    • Amigó, E.1    Gonzalo, J.2    Artiles, J.3    Verdejo, F.4
  • 30
    • 34347388416 scopus 로고    scopus 로고
    • Agreement in breast cancer classification between microarray and quantitative reverse transcription PCR from fresh-frozen and formalin-fixed, paraffin-embedded tissues
    • 10.1373/clinchem.2006.083725, 17525107
    • Mullins M, Perreard L, Quackenbush J, Gauthier N, Bayer S, Ellis M, Parker J, Perou C, Szabo A, Bernard P. Agreement in breast cancer classification between microarray and quantitative reverse transcription PCR from fresh-frozen and formalin-fixed, paraffin-embedded tissues. Clinical chemistry 2007, 53(7):1273. 10.1373/clinchem.2006.083725, 17525107.
    • (2007) Clinical chemistry , vol.53 , Issue.7 , pp. 1273
    • Mullins, M.1    Perreard, L.2    Quackenbush, J.3    Gauthier, N.4    Bayer, S.5    Ellis, M.6    Parker, J.7    Perou, C.8    Szabo, A.9    Bernard, P.10
  • 31
  • 32
    • 59449086167 scopus 로고    scopus 로고
    • The functional loss of the retinoblastoma tumour suppressor is a common event in basal-like and luminal B breast carcinomas
    • 10.1186/bcr2142, 2614508, 18782450
    • Herschkowitz J, He X, Fan C, Perou C. The functional loss of the retinoblastoma tumour suppressor is a common event in basal-like and luminal B breast carcinomas. Breast Cancer Res 2008, 10(5):R75. 10.1186/bcr2142, 2614508, 18782450.
    • (2008) Breast Cancer Res , vol.10 , Issue.5
    • Herschkowitz, J.1    He, X.2    Fan, C.3    Perou, C.4
  • 36
    • 0042567193 scopus 로고    scopus 로고
    • Gene expression profiling identifies molecular subtypes of gliomas
    • 10.1038/sj.onc.1206753, 12894235
    • Shai R, Shi T, Kremen T, Horvath S, Liau L, Cloughesy T, Mischel P, Nelson S. Gene expression profiling identifies molecular subtypes of gliomas. Oncogene 2003, 22(31):4918-4923. 10.1038/sj.onc.1206753, 12894235.
    • (2003) Oncogene , vol.22 , Issue.31 , pp. 4918-4923
    • Shai, R.1    Shi, T.2    Kremen, T.3    Horvath, S.4    Liau, L.5    Cloughesy, T.6    Mischel, P.7    Nelson, S.8
  • 37
    • 0037810449 scopus 로고    scopus 로고
    • Subsystem identification through dimensionality reduction of large-scale gene expression data
    • 10.1101/gr.903503, 403744, 12840046
    • Kim P, Tidor B. Subsystem identification through dimensionality reduction of large-scale gene expression data. Genome Research 2003, 13(7):1706. 10.1101/gr.903503, 403744, 12840046.
    • (2003) Genome Research , vol.13 , Issue.7 , pp. 1706
    • Kim, P.1    Tidor, B.2
  • 38
    • 49849097634 scopus 로고    scopus 로고
    • The relationships among various nonnegative matrix factorization methods for clustering
    • Li T, Ding C. The relationships among various nonnegative matrix factorization methods for clustering. Data Mining, 2006.ICDM'06. Sixth International Conference on 2006, 362-371.
    • (2006) Data Mining, 2006.ICDM'06. Sixth International Conference on , pp. 362-371
    • Li, T.1    Ding, C.2
  • 39
    • 0034934774 scopus 로고    scopus 로고
    • Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association
    • 10.1038/ng569, 11455386
    • Lieb J, Liu X, Botstein D, Brown P. Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nature genetics 2001, 28(4):327-334. 10.1038/ng569, 11455386.
    • (2001) Nature genetics , vol.28 , Issue.4 , pp. 327-334
    • Lieb, J.1    Liu, X.2    Botstein, D.3    Brown, P.4
  • 40
    • 0035945567 scopus 로고    scopus 로고
    • Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF
    • 10.1038/35054095, 11206552
    • Iyer V, Horak C, Scafe C, Botstein D, Snyder M, Brown P. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 2001, 409(6819):533-538. 10.1038/35054095, 11206552.
    • (2001) Nature , vol.409 , Issue.6819 , pp. 533-538
    • Iyer, V.1    Horak, C.2    Scafe, C.3    Botstein, D.4    Snyder, M.5    Brown, P.6
  • 42
    • 0037372003 scopus 로고    scopus 로고
    • Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals
    • 10.1038/ng1089, 12610534
    • Jaenisch R, Bird A. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nature genetics 2003, 33:245-254. 10.1038/ng1089, 12610534.
    • (2003) Nature genetics , vol.33 , pp. 245-254
    • Jaenisch, R.1    Bird, A.2
  • 43
    • 16544373609 scopus 로고    scopus 로고
    • Analysis of transcriptional regulation of the small leucine rich proteoglycans
    • Tasheva E, Klocke B, Conrad G. Analysis of transcriptional regulation of the small leucine rich proteoglycans. Mol Vis 2004, 10:758-772.
    • (2004) Mol Vis , vol.10 , pp. 758-772
    • Tasheva, E.1    Klocke, B.2    Conrad, G.3
  • 44
    • 0030525165 scopus 로고    scopus 로고
    • Gibbs sampling will fail in outlier problems with strong masking
    • Justel A. Gibbs sampling will fail in outlier problems with strong masking. Journal of Computational and Graphical Statistics 1996, 5(2):176-189.
    • (1996) Journal of Computational and Graphical Statistics , vol.5 , Issue.2 , pp. 176-189
    • Justel, A.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.