메뉴 건너뛰기




Volumn 12, Issue 3, 2013, Pages 142-149

Identifying context-specific transcription factor targets from prior knowledge and gene expression data

Author keywords

Bioinformatics; genetic expression; genomics

Indexed keywords

GASTROINTESTINAL STROMAL TUMORS; GENE EXPRESSION DATA; GENETIC EXPRESSIONS; GENOMICS; NUMERICAL EXPERIMENTS; OVERLAPPING GENES; PRIOR PROBABILITY; TRANSCRIPTIONAL RESPONSE;

EID: 84883347632     PISSN: 15361241     EISSN: None     Source Type: Journal    
DOI: 10.1109/TNB.2013.2263390     Document Type: Article
Times cited : (9)

References (20)
  • 1
    • 71549130141 scopus 로고    scopus 로고
    • Detection of treatment-induced changes in signaling pathways in gastrointestinal stromal tumors using transcriptomic data
    • M. F. Ochs, L. Rink, C. Tarn, S. Mburu, T. Taguchi, B. Eisenberg, and A. K. Godwin, "Detection of treatment-induced changes in signaling pathways in gastrointestinal stromal tumors using transcriptomic data, " Cancer Res., vol 69, no. 23, pp. 9125-32, 2009.
    • (2009) Cancer Res , vol.69 , Issue.23 , pp. 9125-32
    • Ochs, M.F.1    Rink, L.2    Tarn, C.3    Mburu, S.4    Taguchi, T.5    Eisenberg, B.6    Godwin, A.K.7
  • 2
    • 70349312354 scopus 로고    scopus 로고
    • Chip-seq: Advantages and challenges of a maturing technology
    • P. J. Park, "Chip-seq: advantages and challenges of a maturing technology, " Nat. Rev. Genet., vol. 10, no. 10, pp. 669-80, 2009.
    • (2009) Nat. Rev. Genet , vol.10 , Issue.10 , pp. 669-80
    • Park, P.J.1
  • 3
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • Encode Project Consortium, "An integrated encyclopedia of DNA elements in the human genome, " Nature, vol. 489, no. 7414, pp. 57-74, 2012.
    • (2012) Nature , vol.489 , Issue.7414 , pp. 57-74
  • 4
    • 44349109637 scopus 로고    scopus 로고
    • Eukaryotic transcription factor binding sites-modeling and integrative search methods
    • S. Hannenhalli, "Eukaryotic transcription factor binding sites-modeling and integrative search methods, " Bioinformatics, vol. 24, pp. 1325-31, 2008.
    • (2008) Bioinformatics , vol.24 , pp. 1325-31
    • Hannenhalli, S.1
  • 5
    • 45249117247 scopus 로고    scopus 로고
    • Identification of Pou5f1, Sox2, and nanog downstream target genes with statistical confidence by applying a novel algorithm to time course microarray and genome-wide chromatin immunoprecipitation data
    • A. A. Sharov, S.Masui, L. V. Sharova, Y. Piao, K. Aiba, R. Matoba, L. Xin, H. Niwa, and M. S. H. Ko, "Identification of Pou5f1, Sox2, and nanog downstream target genes with statistical confidence by applying a novel algorithm to time course microarray and genome-wide chromatin immunoprecipitation data, " BMC Genomics, vol. 9, p. 269, 2008.
    • (2008) BMC Genomics , vol.9 , pp. 269
    • Sharov, A.A.1    Masui, S.2    Sharova, L.V.3    Piao, Y.4    Aiba, K.5    Matoba, R.6    Xin, L.7    Niwa, H.8    Ko, M.S.H.9
  • 6
    • 79954522725 scopus 로고    scopus 로고
    • Large-scale learning of combinatorial transcriptional dynamics from gene expression
    • H. M. S. Asif and G. Sanguinetti, "Large-scale learning of combinatorial transcriptional dynamics from gene expression, " Bioinformatics, vol. 27, no. 9, pp. 1277-83, 2011.
    • (2011) Bioinformatics , vol.27 , Issue.9 , pp. 1277-83
    • Asif, H.M.S.1    Sanguinetti, G.2
  • 7
    • 77954195272 scopus 로고    scopus 로고
    • Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM
    • C. J. Vaske, S. C. Benz, J. Z. Sanborn, D. Earl, C. Szeto, J. Zhu, D. Haussler, and J. M. Stuart, "Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM, " Bioinformatics, vol. 26, no. 12, pp. 237-45, 2010.
    • (2010) Bioinformatics , vol.26 , Issue.12 , pp. 237-45
    • Vaske, C.J.1    Benz, S.C.2    Sanborn, J.Z.3    Earl, D.4    Szeto, C.5    Zhu, J.6    Haussler, D.7    Stuart, J.M.8
  • 8
    • 41449112432 scopus 로고    scopus 로고
    • From promoter analysis to transcriptional regulatory network prediction using PAINT
    • G. E. Gonye, P. Chakravarthula, J. S. Schwaber, and R. Vadigepalli, "From promoter analysis to transcriptional regulatory network prediction using PAINT, " Methods Mol. Biol., vol. 408, pp. 49-68, 2007.
    • (2007) Methods Mol. Biol , vol.408 , pp. 49-68
    • Gonye, G.E.1    Chakravarthula, P.2    Schwaber, J.S.3    Vadigepalli, R.4
  • 9
    • 77951273857 scopus 로고    scopus 로고
    • Matrix factorisation methods applied in microarray data analysis
    • A. V. Kossenkov and M. F. Ochs, "Matrix factorisation methods applied in microarray data analysis, " Int. J. Data Min. Bioinform., vol. 4, no. 1, pp. 72-90, 2010.
    • (2010) Int. J. Data Min. Bioinform , vol.4 , Issue.1 , pp. 72-90
    • Kossenkov, A.V.1    Ochs, M.F.2
  • 10
    • 77958479692 scopus 로고    scopus 로고
    • CoGAPS: An R/C++ package to identify patterns and biological process activity in transcriptomic data
    • E. J. Fertig, J. Ding, A. V. Favorov, G. Parmigiani, and M. F. Ochs, "CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data, " Bioinformatics, vol. 26, no. 21, pp. 2792-3, 2010.
    • (2010) Bioinformatics , vol.26 , Issue.21 , pp. 2792-3
    • Fertig, E.J.1    Ding, J.2    Favorov, A.V.3    Parmigiani, G.4    Ochs, M.F.5
  • 11
    • 35748970508 scopus 로고    scopus 로고
    • Determining transcription factor activity from microarray data using Bayesian Markov chain Monte Carlo sampling
    • A. V. Kossenkov, A. J. Peterson, and M. F. Ochs, "Determining transcription factor activity from microarray data using Bayesian Markov chain Monte Carlo sampling, " Stud. Health Technol. Inform., vol. 129, pt. 2, pp. 1250-4, 2007.
    • (2007) Stud. Health Technol. Inform , vol.129 , Issue.PART 2 , pp. 1250-4
    • Kossenkov, A.V.1    Peterson, A.J.2    Ochs, M.F.3
  • 12
    • 0000676356 scopus 로고    scopus 로고
    • Prior distributions on measure space
    • S. Sibisi and J. Skilling, "Prior distributions on measure space, " J. Roy. Stat. Soc. B, vol. 59, no. 1, pp. 217-235, 1997.
    • (1997) J. Roy. Stat. Soc. B , vol.59 , Issue.1 , pp. 217-235
    • Sibisi, S.1    Skilling, J.2
  • 13
    • 84861832789 scopus 로고    scopus 로고
    • Gene expression signatures modulated by epidermal growth factor receptor activation and their relationship to cetuximab resistance in head and neck squamous cell carcinoma
    • E. J. Fertig, Q. Ren, H. Cheng, H. Hatakeyama, A. Dicker, U. Rodeck, M. Considine, M. F. Ochs, and C. H. Chung, "Gene expression signatures modulated by epidermal growth factor receptor activation and their relationship to cetuximab resistance in head and neck squamous cell carcinoma, " BMC Genomics, vol. 13, p. 160, 2012.
    • (2012) BMC Genomics , vol.13 , pp. 160
    • Fertig, E.J.1    Ren, Q.2    Cheng, H.3    Hatakeyama, H.4    Dicker, A.5    Rodeck, U.6    Considine, M.7    Ochs, M.F.8    Chung, C.H.9
  • 14
    • 0035684378 scopus 로고    scopus 로고
    • A model for measurement error for gene expression arrays
    • D. M. Rocke and B. Durbin, "A model for measurement error for gene expression arrays, " J. Comput. Biol., vol. 8, no. 6, pp. 557-569, 2001.
    • (2001) J. Comput. Biol , vol.8 , Issue.6 , pp. 557-569
    • Rocke, D.M.1    Durbin, B.2
  • 16
    • 79952744274 scopus 로고    scopus 로고
    • Reduce, reuse, and recycle: Developmental evolution of trait diversification
    • J. Preston, L. Hileman, and P. Cubas, "Reduce, reuse, and recycle: Developmental evolution of trait diversification, " Amer. J. Bot., vol. 98, pp. 397-403, 2011.
    • (2011) Amer. J. Bot , vol.98 , pp. 397-403
    • Preston, J.1    Hileman, L.2    Cubas, P.3
  • 17
    • 0037810449 scopus 로고    scopus 로고
    • Subsystem identification through dimensionality reduction of large-scale gene expression data
    • P. M. Kim and B. Tidor, "Subsystem identification through dimensionality reduction of large-scale gene expression data, " Genome Res., vol. 13, no. 7, pp. 1706-18, 2003.
    • (2003) Genome Res , vol.13 , Issue.7 , pp. 1706-18
    • Kim, P.M.1    Tidor, B.2
  • 18
    • 4544341015 scopus 로고    scopus 로고
    • Linear models and empirical bayes methods for assessing differential expression in microarray experiments
    • Article 3
    • G. K. Smyth, "Linear models and empirical bayes methods for assessing differential expression in microarray experiments, " Stat. Appl. Genet. Mol. Biol., vol. 3, 2004, Article 3.
    • (2004) Stat. Appl. Genet. Mol. Biol , vol.3
    • Smyth, G.K.1
  • 20
    • 33646181805 scopus 로고    scopus 로고
    • LS-NMF: A modified non-negative matrix factorization algorithm utilizing uncertainty estimates
    • G. Wang, A. V. Kossenkov, and M. F. Ochs, "LS-NMF: a modified non-negative matrix factorization algorithm utilizing uncertainty estimates, " BMC Bioinformatics, vol. 28, p. 175, 2006.
    • (2006) BMC Bioinformatics , vol.28 , pp. 175
    • Wang, G.1    Kossenkov, A.V.2    Ochs, M.F.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.