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Volumn 12, Issue 2, 2005, Pages 229-246

A statistical method for constructing transcriptional regulatory networks using gene expression and sequence data

Author keywords

Cross validation model selection; Microarray; Mixture model; Multiple testing; Transcriptional regulatory network

Indexed keywords

TRANSCRIPTION FACTOR;

EID: 15944376548     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2005.12.229     Document Type: Article
Times cited : (20)

References (54)
  • 1
    • 0028799428 scopus 로고
    • Mcm1 is required to coordinate G2-specific transcription in Saccharomyces cerevisiae
    • Althoefer, H., Schleiffer, A., Wassmann, K., Nordheim, A., and Ammerer, G. 1995. Mcm1 is required to coordinate G2-specific transcription in Saccharomyces cerevisiae. Mol. Cell Biol. 15, 5917-5928.
    • (1995) Mol. Cell Biol. , vol.15 , pp. 5917-5928
    • Althoefer, H.1    Schleiffer, A.2    Wassmann, K.3    Nordheim, A.4    Ammerer, G.5
  • 3
    • 1942453302 scopus 로고    scopus 로고
    • Predicting gene expression from sequence
    • Beer, M.A., and Tavazoie, S. 2004. Predicting gene expression from sequence. Cell 117, 185-198.
    • (2004) Cell , vol.117 , pp. 185-198
    • Beer, M.A.1    Tavazoie, S.2
  • 4
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini, Y., and Hochberg, Y. 1995. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. Roy. Stat. Soc. Series B 51, 289-300.
    • (1995) J. Roy. Stat. Soc. Series B , vol.51 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 7
    • 0035135420 scopus 로고    scopus 로고
    • Regulatory element detection using correlation with expression
    • Bussemaker, H.J., Li, H., and Siggia, E.D. 2001. Regulatory element detection using correlation with expression. Nature Genet. 27, 167-171.
    • (2001) Nature Genet. , vol.27 , pp. 167-171
    • Bussemaker, H.J.1    Li, H.2    Siggia, E.D.3
  • 8
    • 0032611513 scopus 로고    scopus 로고
    • Modeling gene expression with differential equations
    • Chen, T., He, H.L., and Church, G.M. 1999. Modeling gene expression with differential equations. Proc. Pac. Symp. Biocomput. 4, 29-40.
    • (1999) Proc. Pac. Symp. Biocomput. , vol.4 , pp. 29-40
    • Chen, T.1    He, H.L.2    Church, G.M.3
  • 10
    • 0032037291 scopus 로고    scopus 로고
    • Gametogenesis in yeast is regulated by a transcriptional cascade dependent on ndt80
    • Chu, S., and Herskowitz, I. 1998. Gametogenesis in yeast is regulated by a transcriptional cascade dependent on ndt80. Mol. Cell 1, 685-696.
    • (1998) Mol. Cell , vol.1 , pp. 685-696
    • Chu, S.1    Herskowitz, I.2
  • 11
    • 0037453009 scopus 로고    scopus 로고
    • Integrating sequence motif discovery and microarray analysis
    • Conlon, E.M., Liu, X.S., Lieb, J.D., and Liu, J.S. 2003. Integrating sequence motif discovery and microarray analysis, Proc. Natl. Acad. Sci. 100, 3339-3344.
    • (2003) Proc. Natl. Acad. Sci. , vol.100 , pp. 3339-3344
    • Conlon, E.M.1    Liu, X.S.2    Lieb, J.D.3    Liu, J.S.4
  • 12
    • 0028898763 scopus 로고
    • Multiple elements and auto-repression regulate rox1, a repressor of hypoxic genes in Saccharomyces cerevisiae
    • Deckert, J., Perini, R., Balasubramanian, B., and Zitomer, R.S. 1995. Multiple elements and auto-repression regulate rox1, a repressor of hypoxic genes in Saccharomyces cerevisiae. Genetics 139, 1149-1158.
    • (1995) Genetics , vol.139 , pp. 1149-1158
    • Deckert, J.1    Perini, R.2    Balasubramanian, B.3    Zitomer, R.S.4
  • 13
    • 0029042698 scopus 로고
    • Positive autoregulation of the yeast transcription factor pdr3p, which is involved in control of drug resistance
    • Delahodde, A., Delaveau, T., and Jacq, C. 1995. Positive autoregulation of the yeast transcription factor pdr3p, which is involved in control of drug resistance. Mol. Cell Biol. 15, 4043-4051.
    • (1995) Mol. Cell Biol. , vol.15 , pp. 4043-4051
    • Delahodde, A.1    Delaveau, T.2    Jacq, C.3
  • 15
    • 0030669030 scopus 로고    scopus 로고
    • Exploring the metabolic and genetic control of gene expression on a genomic scale
    • DeRisi, J.L., Iyer, V.R., and Brown, P.O. 1997. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278, 680-686.
    • (1997) Science , vol.278 , pp. 680-686
    • DeRisi, J.L.1    Iyer, V.R.2    Brown, P.O.3
  • 16
    • 0033736476 scopus 로고    scopus 로고
    • Genetic network inference: From co-expression clustering to reverse engineering
    • D'Haeseleer, P., Liang, S., and Somogyi, R. 2000. Genetic network inference: From co-expression clustering to reverse engineering. Bioinformatics 16, 707-726.
    • (2000) Bioinformatics , vol.16 , pp. 707-726
    • D'Haeseleer, P.1    Liang, S.2    Somogyi, R.3
  • 17
    • 0032612220 scopus 로고    scopus 로고
    • Linear modeling of mRNA expression levels during cns development and injury
    • D'Haeseleer, P., Wen, X., Fuhrman, S., and Somogyi, R. 1999. Linear modeling of mRNA expression levels during cns development and injury. Proc. Pac. Symp. Biocomputing 4, 41-52.
    • (1999) Proc. Pac. Symp. Biocomputing , vol.4 , pp. 41-52
    • D'Haeseleer, P.1    Wen, X.2    Fuhrman, S.3    Somogyi, R.4
  • 19
    • 0033578424 scopus 로고    scopus 로고
    • Systematic changes in gene expression patterns following adaptive evolution in yeast
    • Ferea, T.L., Botstein, D., Brown, P.O., and Rosenzweig, R.F. 1999. Systematic changes in gene expression patterns following adaptive evolution in yeast. Proc. Natl. Acad. Sci. 96 (17), 9721-9726.
    • (1999) Proc. Natl. Acad. Sci. , vol.96 , Issue.17 , pp. 9721-9726
    • Ferea, T.L.1    Botstein, D.2    Brown, P.O.3    Rosenzweig, R.F.4
  • 20
    • 0037815412 scopus 로고    scopus 로고
    • Mcm7, a subunit of the presumptive mem helicase, modulates its own expression in conjunction with mcm1
    • Fitch, M.J., Donato, J.J., and Tye, B.K. 2003. Mcm7, a subunit of the presumptive mem helicase, modulates its own expression in conjunction with mcm1. J. Biol. Chem. 278, 25408-25416.
    • (2003) J. Biol. Chem. , vol.278 , pp. 25408-25416
    • Fitch, M.J.1    Donato, J.J.2    Tye, B.K.3
  • 21
    • 0033707946 scopus 로고    scopus 로고
    • Using Bayesian networks to analyze expression data
    • Friedman, N., Linial, M., Nachman, L. and Pe'er, D. 2000. Using Bayesian networks to analyze expression data. J. Comp. Biol. 7, 601-620.
    • (2000) J. Comp. Biol. , vol.7 , pp. 601-620
    • Friedman, N.1    Linial, M.2    Nachman, L.3    Pe'er, D.4
  • 22
    • 0035162698 scopus 로고    scopus 로고
    • Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog mec1p
    • Gasch, A.P., Huang, M., Metzner, S., Botstein, D., Elledge, S.J., and Brown, P.O. 2001. Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog mec1p. Mol. Biol. Cell 12, 2987-3003.
    • (2001) Mol. Biol. Cell , vol.12 , pp. 2987-3003
    • Gasch, A.P.1    Huang, M.2    Metzner, S.3    Botstein, D.4    Elledge, S.J.5    Brown, P.O.6
  • 24
    • 0028362731 scopus 로고
    • A reb1p-binding site is required for efficient activation of the yeast rap1 gene, but multiple binding sites for rap1p are not essential
    • Graham, I.R., and Chambers, A. 1994. A reb1p-binding site is required for efficient activation of the yeast rap1 gene, but multiple binding sites for rap1p are not essential. Mol. Microbiol. 12, 931-940.
    • (1994) Mol. Microbiol. , vol.12 , pp. 931-940
    • Graham, I.R.1    Chambers, A.2
  • 25
    • 0034644739 scopus 로고    scopus 로고
    • Identification of the copper regulon in Saccharomyces cerevisiae by DNA microarrays
    • Gross, C., Kelleher, M., Iyer, V.R., Brown, P.O., and Winge, D.R. 2000. Identification of the copper regulon in Saccharomyces cerevisiae by DNA microarrays. J. Biol. Chem. 275, 32310-32316.
    • (2000) J. Biol. Chem. , vol.275 , pp. 32310-32316
    • Gross, C.1    Kelleher, M.2    Iyer, V.R.3    Brown, P.O.4    Winge, D.R.5
  • 27
    • 0032894060 scopus 로고    scopus 로고
    • Yeast proteome database (ypd): A model for the organization and presentation of genome-wide functional data
    • Hodges, P.E., McKee, A.H.Z., Davis, B.P., Payne, W.E., and Garrels, J.I. 1999. Yeast proteome database (ypd): A model for the organization and presentation of genome-wide functional data. Nucl. Acids Res. 27, 69-73.
    • (1999) Nucl. Acids Res. , vol.27 , pp. 69-73
    • Hodges, P.E.1    McKee, A.H.Z.2    Davis, B.P.3    Payne, W.E.4    Garrels, J.I.5
  • 29
    • 0036740483 scopus 로고    scopus 로고
    • Identification of regulatory elements using a feature selection method
    • Keles, S., van der Laan, M.J., and Eisen, M.B. 2002. Identification of regulatory elements using a feature selection method. Bioinformatics 18, 1167-1175.
    • (2002) Bioinformatics , vol.18 , pp. 1167-1175
    • Keles, S.1    Van Der Laan, M.J.2    Eisen, M.B.3
  • 31
    • 0031616241 scopus 로고    scopus 로고
    • Reveal: A general reverse engineering algorithm for inference of genetic network architectures
    • Liang, S., Fuhrman, S., and Somogyi, R. 1998. Reveal: A general reverse engineering algorithm for inference of genetic network architectures. Proc. Pac. Symp. Biocomput. 3, 18-29.
    • (1998) Proc. Pac. Symp. Biocomput. , vol.3 , pp. 18-29
    • Liang, S.1    Fuhrman, S.2    Somogyi, R.3
  • 32
    • 0034405703 scopus 로고    scopus 로고
    • The pachytene checkpoint in Saccharomyces cerevisiae requires the sum1 transcriptional repressor
    • Lindgren, A., Bungard, D., Pierce, M., Xie, J., Vershon, A., and Winter, E. 2000. The pachytene checkpoint in Saccharomyces cerevisiae requires the sum1 transcriptional repressor. Embo. J. 19, 6489-6497.
    • (2000) Embo. J. , vol.19 , pp. 6489-6497
    • Lindgren, A.1    Bungard, D.2    Pierce, M.3    Xie, J.4    Vershon, A.5    Winter, E.6
  • 33
    • 0033597892 scopus 로고    scopus 로고
    • Distinct regions of the swi5 and ace2 transcription factors are required for specific gene activation
    • McBride, H.J., Yu, Y., and Stillman, D.J. 1999. Distinct regions of the swi5 and ace2 transcription factors are required for specific gene activation. J. Biol. Chem. 274, 21029-21036.
    • (1999) J. Biol. Chem. , vol.274 , pp. 21029-21036
    • McBride, H.J.1    Yu, Y.2    Stillman, D.J.3
  • 34
    • 0033637520 scopus 로고    scopus 로고
    • New components of a system for phosphate accumulation and polyphosphate metabolism in Saccharomyces cerevisiae revealed by genomic expression analysis
    • Ogawa, N., DeRisi, J., and Brown, P.O. 2000. New components of a system for phosphate accumulation and polyphosphate metabolism in Saccharomyces cerevisiae revealed by genomic expression analysis. Mol. Biol. Cell 11, 4309-4321.
    • (2000) Mol. Biol. Cell , vol.11 , pp. 4309-4321
    • Ogawa, N.1    DeRisi, J.2    Brown, P.O.3
  • 35
    • 0036723646 scopus 로고    scopus 로고
    • Regulation of the premiddle and middle phases of expression of the ndt80 gene during sporulation Saccharomyces cerevisiae
    • Pak, J., and Segall, J. 2002. Regulation of the premiddle and middle phases of expression of the ndt80 gene during sporulation Saccharomyces cerevisiae. Mol. Cell Biol. 22, 6417-6429.
    • (2002) Mol. Cell Biol. , vol.22 , pp. 6417-6429
    • Pak, J.1    Segall, J.2
  • 36
    • 0034785443 scopus 로고    scopus 로고
    • Identifying regulatory networks by combinatorial analysis of promoter elements
    • Pilpel, Y., Sudarsanam, P., and Church, G. 2001. Identifying regulatory networks by combinatorial analysis of promoter elements. Nature Genet. 29, 153-159.
    • (2001) Nature Genet. , vol.29 , pp. 153-159
    • Pilpel, Y.1    Sudarsanam, P.2    Church, G.3
  • 37
    • 0142179209 scopus 로고    scopus 로고
    • Prediction of regulatory networks: Genome-wide identification of transcription factor targets from gene expression data
    • Qian, J., Lin, J., Luscombe, N.M., Yu, H., and Gerstein, M. 2003. Prediction of regulatory networks: Genome-wide identification of transcription factor targets from gene expression data. Bioinformatics 19, 1917-1926.
    • (2003) Bioinformatics , vol.19 , pp. 1917-1926
    • Qian, J.1    Lin, J.2    Luscombe, N.M.3    Yu, H.4    Gerstein, M.5
  • 39
    • 2442446708 scopus 로고    scopus 로고
    • Genome-wide discovery of transcriptional modules from DNA sequence and gene expression
    • Segal, E., Yelensky, R., and Koller, D. 2003. Genome-wide discovery of transcriptional modules from DNA sequence and gene expression. Bioinformatics 19, i273-i282.
    • (2003) Bioinformatics , vol.19
    • Segal, E.1    Yelensky, R.2    Koller, D.3
  • 40
    • 0033637226 scopus 로고    scopus 로고
    • Isolation and molecular characterization of the carboxy-terminal pdr3 mutants in Saccharomyces cerevisiae
    • Simonics, T., Kozovska, Z., Michalkova-Papajova, D., Delahodde, A., Jacq, C., and Subik, J. 2000. Isolation and molecular characterization of the carboxy-terminal pdr3 mutants in Saccharomyces cerevisiae. Curr. Genet. 38, 248-255.
    • (2000) Curr. Genet. , vol.38 , pp. 248-255
    • Simonics, T.1    Kozovska, Z.2    Michalkova-Papajova, D.3    Delahodde, A.4    Jacq, C.5    Subik, J.6
  • 43
    • 0345822598 scopus 로고    scopus 로고
    • The positive false discovery rate: A Bayesian interpretation and the q-value
    • Storey, J.D. 2003. The positive false discovery rate: A Bayesian interpretation and the q-value. Annals Statist. 31, 2013-2035.
    • (2003) Annals Statist. , vol.31 , pp. 2013-2035
    • Storey, J.D.1
  • 44
    • 0034724394 scopus 로고    scopus 로고
    • Whole-genome expression analysis of snf/swi mutants of Saccharomyces cerevisiae
    • Sudarsanam, P., Iyer, V.R., Brown, P.O., and Winston, F. 2000. Whole-genome expression analysis of snf/swi mutants of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. 97, 3364-3369.
    • (2000) Proc. Natl. Acad. Sci. , vol.97 , pp. 3364-3369
    • Sudarsanam, P.1    Iyer, V.R.2    Brown, P.O.3    Winston, F.4
  • 45
    • 0028867670 scopus 로고
    • Review: Compilation and characteristics of dedicated transcription factors in Saccharomyces cerevisiae
    • Svetlov, V.V., and Cooper, T.G. 1995. Review: Compilation and characteristics of dedicated transcription factors in Saccharomyces cerevisiae. Yeast 11, 1439-1484.
    • (1995) Yeast , vol.11 , pp. 1439-1484
    • Svetlov, V.V.1    Cooper, T.G.2
  • 46
    • 0028879611 scopus 로고
    • Rme1, a negative regulator of meiosis, is also a positive activator of g1 cyclin gene expression
    • Toone, W.M., Johnson, A.L., Banks, G.R., Toyn, J.H., Stuart, D., Wittenberg, C., and Johnston, L.H. 1995. Rme1, a negative regulator of meiosis, is also a positive activator of g1 cyclin gene expression. Embo. J. 14, 5824-5832.
    • (1995) Embo. J. , vol.14 , pp. 5824-5832
    • Toone, W.M.1    Johnson, A.L.2    Banks, G.R.3    Toyn, J.H.4    Stuart, D.5    Wittenberg, C.6    Johnston, L.H.7
  • 47
    • 14644419415 scopus 로고    scopus 로고
    • Unified cross-validation methodology for selection among estimators and a general cross-validated adaptive epsilon-net estimator: Finite sample oracle inequalities and examples
    • van der Laan, M.J., and Dudoit, S. 2003. Unified cross-validation methodology for selection among estimators and a general cross-validated adaptive epsilon-net estimator: Finite sample oracle inequalities and examples. UC Berkeley Division of Biostatistics Working Paper Series 130.
    • (2003) UC Berkeley Division of Biostatistics Working Paper Series , pp. 130
    • Van Der Laan, M.J.1    Dudoit, S.2
  • 49
    • 15944399539 scopus 로고    scopus 로고
    • Multiple Testing. Part iii. Procedures for control of the generalized family-wise error rate and proportion of false positives
    • van der Laan, M.J., Dudoit, S., and Pollard, K.S. 2004. Multiple Testing. Part iii. Procedures for control of the generalized family-wise error rate and proportion of false positives. UC Berkeley Division of Biostatistics Working Paper Series 141.
    • (2004) UC Berkeley Division of Biostatistics Working Paper Series , pp. 141
    • Van Der Laan, M.J.1    Dudoit, S.2    Pollard, K.S.3
  • 50
    • 0037168519 scopus 로고    scopus 로고
    • A systematic approach to reconstructing transcription networks in Saccharomyces cerevisiae
    • Wang, W., Cherry, J.M., Botstein, D., and Li, H. 2002. A systematic approach to reconstructing transcription networks in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. 99, 16893-16898.
    • (2002) Proc. Natl. Acad. Sci. , vol.99 , pp. 16893-16898
    • Wang, W.1    Cherry, J.M.2    Botstein, D.3    Li, H.4
  • 51
    • 0029960055 scopus 로고    scopus 로고
    • Transfac: A database on transcription factors and their DNA binding sites
    • Wingender, E., Dietze, P., Karas, H., and Knüppel, R. 1996. Transfac: A database on transcription factors and their DNA binding sites. Nucl. Acids Res. 24, 238-241.
    • (1996) Nucl. Acids Res. , vol.24 , pp. 238-241
    • Wingender, E.1    Dietze, P.2    Karas, H.3    Knüppel, R.4
  • 52
    • 0036358442 scopus 로고    scopus 로고
    • Discovery of causal relationships in a gene-regulation pathway from a mixture of experimental and observational DNA microarray data
    • Yoo, C., Thorsson, V., and Cooper, G.F. 2002, Discovery of causal relationships in a gene-regulation pathway from a mixture of experimental and observational DNA microarray data. Proc. Pac. Symp. Biocomput. 7, 498-509,
    • (2002) Proc. Pac. Symp. Biocomput. , vol.7 , pp. 498-509
    • Yoo, C.1    Thorsson, V.2    Cooper, G.F.3
  • 54
    • 0032861774 scopus 로고    scopus 로고
    • Scpd: A promoter database of yeast Saccharomyces cerevisiae
    • Zhu, J., and Zhang, M.Q. 1999. Scpd: A promoter database of yeast Saccharomyces cerevisiae. Bioinformatics 15, 607-611.
    • (1999) Bioinformatics , vol.15 , pp. 607-611
    • Zhu, J.1    Zhang, M.Q.2


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