메뉴 건너뛰기




Volumn 41, Issue 6, 2008, Pages 914-926

Consensus and Meta-analysis regulatory networks for combining multiple microarray gene expression datasets

Author keywords

Bayesian networks; Consensus algorithms; Gene regulatory networks; Meta analysis; Microarray gene expression data

Indexed keywords

AGGLOMERATION; BIOACTIVITY; DATA REDUCTION; DISTRIBUTED PARAMETER NETWORKS; EDUCATION; ESCHERICHIA COLI; GENE EXPRESSION; INFERENCE ENGINES; INTELLIGENT NETWORKS; MODAL ANALYSIS; SPEECH ANALYSIS; SPEECH RECOGNITION;

EID: 55549111910     PISSN: 15320464     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbi.2008.01.011     Document Type: Article
Times cited : (27)

References (39)
  • 1
    • 0033707946 scopus 로고    scopus 로고
    • Using Bayesian networks to analyze expression data
    • Friedman N., Linial M., Nachman I., and Pe'er D. Using Bayesian networks to analyze expression data. J Comput Biol 7 3-4 (2000) 601-620
    • (2000) J Comput Biol , vol.7 , Issue.3-4 , pp. 601-620
    • Friedman, N.1    Linial, M.2    Nachman, I.3    Pe'er, D.4
  • 2
    • 0036522639 scopus 로고    scopus 로고
    • Bayesian methods for elucidating genetic regulatory networks
    • Hartemink A.J., Gifford D., Jaakkola T., and Young R. Bayesian methods for elucidating genetic regulatory networks. IEEE Intell Syst 17 2 (2002) 37-43
    • (2002) IEEE Intell Syst , vol.17 , Issue.2 , pp. 37-43
    • Hartemink, A.J.1    Gifford, D.2    Jaakkola, T.3    Young, R.4
  • 3
    • 33646338193 scopus 로고    scopus 로고
    • MinReg: a scalable algorithm for learning parsimonious networks in yeast and mammals
    • Pe'er D., Tanay A., and Regev A. MinReg: a scalable algorithm for learning parsimonious networks in yeast and mammals. J Mach Learn Res 7 (2006) 167-189
    • (2006) J Mach Learn Res , vol.7 , pp. 167-189
    • Pe'er, D.1    Tanay, A.2    Regev, A.3
  • 4
    • 0348136790 scopus 로고    scopus 로고
    • Supervised classification for gene network reconstruction
    • Soinov L.A. Supervised classification for gene network reconstruction. Biochem Soc Trans 31 6 (2003) 1497-1502
    • (2003) Biochem Soc Trans , vol.31 , Issue.6 , pp. 1497-1502
    • Soinov, L.A.1
  • 5
    • 0036211063 scopus 로고    scopus 로고
    • Analysis of matched mRNA measurements from two different microarray technologies
    • Kuo W.P., Jenssen T.K., Butte A.J., Ohno-Machado L., and Kohane I.S. Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics 18 3 (2002) 405-412
    • (2002) Bioinformatics , vol.18 , Issue.3 , pp. 405-412
    • Kuo, W.P.1    Jenssen, T.K.2    Butte, A.J.3    Ohno-Machado, L.4    Kohane, I.S.5
  • 10
    • 14944364222 scopus 로고    scopus 로고
    • On combining multiple microarray studies for improved functional classification by whole-dataset feature selection
    • Ng S.K., Tan S.H., and Sundararajan V.S. On combining multiple microarray studies for improved functional classification by whole-dataset feature selection. Genome Inform 14 (2003) 44-53
    • (2003) Genome Inform , vol.14 , pp. 44-53
    • Ng, S.K.1    Tan, S.H.2    Sundararajan, V.S.3
  • 11
    • 33747017793 scopus 로고    scopus 로고
    • Bayesian models for pooling microarray studies with multiple sources of replications
    • Conlon E.M., Song J.J., and Liu J.S. Bayesian models for pooling microarray studies with multiple sources of replications. BMC Bioinform 7 247 (2006)
    • (2006) BMC Bioinform , vol.7 , Issue.247
    • Conlon, E.M.1    Song, J.J.2    Liu, J.S.3
  • 12
    • 33750016109 scopus 로고    scopus 로고
    • Inferring gene regulatory networks from multiple microarray datasets
    • Wang Y., Joshi T., Zhang X.S., Xu D., and Chen L. Inferring gene regulatory networks from multiple microarray datasets. Bioinformatics 22 19 (2006) 2413-2420
    • (2006) Bioinformatics , vol.22 , Issue.19 , pp. 2413-2420
    • Wang, Y.1    Joshi, T.2    Zhang, X.S.3    Xu, D.4    Chen, L.5
  • 13
    • 4744369980 scopus 로고    scopus 로고
    • On information criteria and the generalized likelihood ratio test of model order selection
    • Stoica P. On information criteria and the generalized likelihood ratio test of model order selection. IEEE Signal Process Lett 11 10 (2004)
    • (2004) IEEE Signal Process Lett , vol.11 , Issue.10
    • Stoica, P.1
  • 14
    • 0016355478 scopus 로고
    • A new look at the statistical model identification
    • Akaike H. A new look at the statistical model identification. IEEE Trans Automatic Control 19 6 (1974) 716-723
    • (1974) IEEE Trans Automatic Control , vol.19 , Issue.6 , pp. 716-723
    • Akaike, H.1
  • 16
    • 55549138647 scopus 로고    scopus 로고
    • Chickering D. A transformational characterization of equivalent Bayesian network structures. In: Proceedings of uncertainty in artificial intelligence, vol. 11; 1995.
    • Chickering D. A transformational characterization of equivalent Bayesian network structures. In: Proceedings of uncertainty in artificial intelligence, vol. 11; 1995.
  • 17
    • 55549147785 scopus 로고    scopus 로고
    • Friedman N, Goldszmidt M, Wyner A. Data analysis with Bayesian networks: a bootstrap approach. In: Proceedings of 15th annual conference on uncertainty in artificial intelligence; 1999.
    • Friedman N, Goldszmidt M, Wyner A. Data analysis with Bayesian networks: a bootstrap approach. In: Proceedings of 15th annual conference on uncertainty in artificial intelligence; 1999.
  • 18
    • 55549083421 scopus 로고    scopus 로고
    • Efron B, Tibshirani R. An introduction to the Bootstrap; 1993.
    • Efron B, Tibshirani R. An introduction to the Bootstrap; 1993.
  • 19
    • 0242333835 scopus 로고    scopus 로고
    • Normalization of cDNA microarray data
    • Smyth G., and Speed T. Normalization of cDNA microarray data. Methods 31 (2003) 265-273
    • (2003) Methods , vol.31 , pp. 265-273
    • Smyth, G.1    Speed, T.2
  • 20
    • 34547315736 scopus 로고    scopus 로고
    • Park D, Wang X. Toward a general framework for microarray data comparison. In: Proceedings of the 6th IEEE international conference on computer and information technology (CIT'06); 2006.
    • Park D, Wang X. Toward a general framework for microarray data comparison. In: Proceedings of the 6th IEEE international conference on computer and information technology (CIT'06); 2006.
  • 23
    • 18144442687 scopus 로고    scopus 로고
    • Inferring subnetworks from perturbed expression profiles
    • Pe'er D., Regev A., Elidan G., and Friedman N. Inferring subnetworks from perturbed expression profiles. Bioinformatics 1 1 (2001) 1-9
    • (2001) Bioinformatics , vol.1 , Issue.1 , pp. 1-9
    • Pe'er, D.1    Regev, A.2    Elidan, G.3    Friedman, N.4
  • 24
    • 40249117001 scopus 로고    scopus 로고
    • Peeling E, Tucker A. Consensus gene regulatory networks: combining multiple microarray gene expression datasets. In: AIP conference proceedings, vol. 940. The 3rd international symposium on computational life sciences (COMPLIFE 2007); 2007.
    • Peeling E, Tucker A. Consensus gene regulatory networks: combining multiple microarray gene expression datasets. In: AIP conference proceedings, vol. 940. The 3rd international symposium on computational life sciences (COMPLIFE 2007); 2007.
  • 25
  • 27
    • 33644873683 scopus 로고    scopus 로고
    • The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae
    • Teixeira M., Monteiro P., Jain P., Tenreiro S., Fernandes A.R., Mira N.P., et al. The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae. Nucleic Acids Res 34 (2006) D446-D451
    • (2006) Nucleic Acids Res , vol.34
    • Teixeira, M.1    Monteiro, P.2    Jain, P.3    Tenreiro, S.4    Fernandes, A.R.5    Mira, N.P.6
  • 28
    • 33846400424 scopus 로고    scopus 로고
    • Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles
    • Faith J.J., Hayete B., Thaden J.T., Mogno I., Wierzbowski J., Cottarel G., et al. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol 5 1 (2007)
    • (2007) PLoS Biol , vol.5 , Issue.1
    • Faith, J.J.1    Hayete, B.2    Thaden, J.T.3    Mogno, I.4    Wierzbowski, J.5    Cottarel, G.6
  • 29
    • 0020083498 scopus 로고
    • The meaning and use of the area under a receiver operating characteristic (ROC) curve
    • Hanley J.A., and McNeil B.J. The meaning and use of the area under a receiver operating characteristic (ROC) curve. Radiology 143 (1982) 29-36
    • (1982) Radiology , vol.143 , pp. 29-36
    • Hanley, J.A.1    McNeil, B.J.2
  • 30
    • 0141532928 scopus 로고    scopus 로고
    • DNA array analysis of gene expression in response to UV irradiation in Escherichia coli
    • Quillardet P., Rouffaud M.A., and Bouige P. DNA array analysis of gene expression in response to UV irradiation in Escherichia coli. Res Microbiol 154 (2003) 559-572
    • (2003) Res Microbiol , vol.154 , pp. 559-572
    • Quillardet, P.1    Rouffaud, M.A.2    Bouige, P.3
  • 31
    • 0035023305 scopus 로고    scopus 로고
    • Comparative gene expression profiles following UV exposure in wild-type and SOS-deficient Escherichia coli
    • Courcelle J., Khodursky A., Peter B., Brown P.O., and Hanawalt P.C. Comparative gene expression profiles following UV exposure in wild-type and SOS-deficient Escherichia coli. Genetics 158 1 (2001) 41-64
    • (2001) Genetics , vol.158 , Issue.1 , pp. 41-64
    • Courcelle, J.1    Khodursky, A.2    Peter, B.3    Brown, P.O.4    Hanawalt, P.C.5
  • 32
    • 0036224939 scopus 로고    scopus 로고
    • Over 1000 genes are involved in the DNA damage response of Escherichia coli
    • Khil P., and Camerini-Otero R. Over 1000 genes are involved in the DNA damage response of Escherichia coli. Mol Microbiol 44 1 (2002) 89-105
    • (2002) Mol Microbiol , vol.44 , Issue.1 , pp. 89-105
    • Khil, P.1    Camerini-Otero, R.2
  • 33
    • 33745022557 scopus 로고    scopus 로고
    • A classification based framework for quantitative description of large-scale microarray data
    • Sangurdekar D., Srienc F., and Khodursky A.B. A classification based framework for quantitative description of large-scale microarray data. Genome Biol 7 (2006)
    • (2006) Genome Biol , vol.7
    • Sangurdekar, D.1    Srienc, F.2    Khodursky, A.B.3
  • 34
    • 55549084444 scopus 로고    scopus 로고
    • Peeling E, Tucker A, t'Hoen P.A.C. Discovery of local regulatory structure from microarray gene expression data using Bayesian networks. In: Proceedings of the annual workshop on intelligent data analysis in biomedicine and pharmacology (IDAMAP); 2007.
    • Peeling E, Tucker A, t'Hoen P.A.C. Discovery of local regulatory structure from microarray gene expression data using Bayesian networks. In: Proceedings of the annual workshop on intelligent data analysis in biomedicine and pharmacology (IDAMAP); 2007.
  • 36
    • 0032441150 scopus 로고    scopus 로고
    • Cluster analysis and display of genome-wide expression patterns
    • Eisen M.B., Spellman P.T., Brown P.O., and Botstein D. Cluster analysis and display of genome-wide expression patterns. PNAS 95 25 (1998) 14863-14868
    • (1998) PNAS , vol.95 , Issue.25 , pp. 14863-14868
    • Eisen, M.B.1    Spellman, P.T.2    Brown, P.O.3    Botstein, D.4
  • 37
    • 0033637153 scopus 로고    scopus 로고
    • Genomic expression program in the response of yeast cells to environmental changes
    • Gasch A., Spellman P., Kao C., Carmel-Harel O., Eisen M., Storz G., et al. Genomic expression program in the response of yeast cells to environmental changes. Mol Cell 11 (2000) 4241-4257
    • (2000) Mol Cell , vol.11 , pp. 4241-4257
    • Gasch, A.1    Spellman, P.2    Kao, C.3    Carmel-Harel, O.4    Eisen, M.5    Storz, G.6
  • 38
    • 2942561052 scopus 로고    scopus 로고
    • Genome-wide analysis of mrna stability using transcription inhibitors and microarrays reveals post-transcriptional control of ribosome biogenesis factors
    • Grigull J., Mnaimneh S., Pootoolal J., Robinson M.D., and Hughes T.R. Genome-wide analysis of mrna stability using transcription inhibitors and microarrays reveals post-transcriptional control of ribosome biogenesis factors. Mol Cell 24 12 (2004) 5534-5547
    • (2004) Mol Cell , vol.24 , Issue.12 , pp. 5534-5547
    • Grigull, J.1    Mnaimneh, S.2    Pootoolal, J.3    Robinson, M.D.4    Hughes, T.R.5
  • 39
    • 0031742022 scopus 로고    scopus 로고
    • Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization
    • Spellman P., Sherlock G., Zhang M., Iyer V., Anders K., Eisen M., et al. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Cell 9 (1998) 3273-3297
    • (1998) Mol Cell , vol.9 , pp. 3273-3297
    • Spellman, P.1    Sherlock, G.2    Zhang, M.3    Iyer, V.4    Anders, K.5    Eisen, M.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.