메뉴 건너뛰기




Volumn 32, Issue 1, 2004, Pages 179-188

Computational inference of transcriptional regulatory networks from expression profiling and transcription factor binding site identification

Author keywords

[No Author keywords available]

Indexed keywords

DNA; TRANSCRIPTION FACTOR; SACCHAROMYCES CEREVISIAE PROTEIN;

EID: 1242342957     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh183     Document Type: Article
Times cited : (76)

References (45)
  • 1
    • 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. Pac. Symp. Biocomput., 18-29.
    • (1998) Pac. Symp. Biocomput. , pp. 18-29
    • Liang, S.1    Fuhrman, S.2    Somogyi, R.3
  • 2
    • 0034570872 scopus 로고    scopus 로고
    • A gene network inference method from continuous-value gene expression data of wild-type and mutants
    • Kyoda,K.M., Morohashi,M., Onami,S. and Kitano,H. (2000) A gene network inference method from continuous-value gene expression data of wild-type and mutants. Genome Inform. Ser. Workshop Genome Inform., 11, 196-204.
    • (2000) Genome Inform. Ser. Workshop Genome Inform. , vol.11 , pp. 196-204
    • Kyoda, K.M.1    Morohashi, M.2    Onami, S.3    Kitano, H.4
  • 3
    • 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
  • 5
    • 0345928693 scopus 로고    scopus 로고
    • Building and analysing genome-wide gene disruption networks
    • Rung,J., Schlitt,T., Brazma,A., Freivalds,K. and Vilo,J. (2002) Building and analysing genome-wide gene disruption networks. Bioinformatics, 18 (Suppl. 2). S202-210.
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 2
    • Rung, J.1    Schlitt, T.2    Brazma, A.3    Freivalds, K.4    Vilo, J.5
  • 6
    • 0037270514 scopus 로고    scopus 로고
    • Towards reconstruction of gene networks from expression data by supervised learning
    • Soinov,L.A., Krestyaninova,M.A. and Brazma,A. (2003) Towards reconstruction of gene networks from expression data by supervised learning. Genome Biol., 4, R6.
    • (2003) Genome Biol. , vol.4
    • Soinov, L.A.1    Krestyaninova, M.A.2    Brazma, A.3
  • 7
    • 0141993704 scopus 로고    scopus 로고
    • A gene-coexpression network for global discovery of conserved genetic modules
    • Stuart,J.M., Segal,E., Koller,D. and Kim,S.K. (2003) A gene-coexpression network for global discovery of conserved genetic modules. Science, 302, 249-255.
    • (2003) Science , vol.302 , pp. 249-255
    • Stuart, J.M.1    Segal, E.2    Koller, D.3    Kim, S.K.4
  • 8
    • 0038281506 scopus 로고    scopus 로고
    • Inference of transcriptional regulation relationships from gene expression data
    • Kwon,A.T., Hoos,H.H. and Ng,R. (2003) Inference of transcriptional regulation relationships from gene expression data. Bioinformatics, 19, 905-912.
    • (2003) Bioinformatics , vol.19 , pp. 905-912
    • Kwon, A.T.1    Hoos, H.H.2    Ng, R.3
  • 9
    • 0037941585 scopus 로고    scopus 로고
    • Module networks: Identifying regulatory modules and their condition-specific regulators from gene expression data
    • Segal,E., Shapira,M., Regev,A., Pe'er,D., Botstein,D., Koller,D. and Friedman,N. (2003) Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nature Genet., 34, 166-176.
    • (2003) Nature Genet. , vol.34 , pp. 166-176
    • Segal, E.1    Shapira, M.2    Regev, A.3    Pe'er, D.4    Botstein, D.5    Koller, D.6    Friedman, N.7
  • 10
    • 0842309161 scopus 로고    scopus 로고
    • Discovering molecular pathways from protein interaction and gene expression data
    • Segal,E., Wang,H. and Koller,D. (2003) Discovering molecular pathways from protein interaction and gene expression data. Bioinformatics, 19 (Suppl. 1), I264-I272.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 1
    • Segal, E.1    Wang, H.2    Koller, D.3
  • 11
    • 0032413411 scopus 로고    scopus 로고
    • Predicting gene regulatory elements in silico on a genomic scale
    • Brazma,A., Jonassen,I., Vilo,J. and Ukkonen,E. (1998) Predicting gene regulatory elements in silico on a genomic scale. Genome Res., 8, 1202-1215.
    • (1998) Genome Res. , vol.8 , pp. 1202-1215
    • Brazma, A.1    Jonassen, I.2    Vilo, J.3    Ukkonen, E.4
  • 12
    • 0032848435 scopus 로고    scopus 로고
    • Candidate regulatory sequence elements for cell cycle-dependent transcription in Saccharomyces cerevisiae
    • Wolfsberg,T.G., Gabrielian,A.E., Campbell,M.J., Cho,R.J., Spouge,J.L. and Landsman,D. (1999) Candidate regulatory sequence elements for cell cycle-dependent transcription in Saccharomyces cerevisiae. Genome Res., 9, 775-792.
    • (1999) Genome Res. , vol.9 , pp. 775-792
    • Wolfsberg, T.G.1    Gabrielian, A.E.2    Campbell, M.J.3    Cho, R.J.4    Spouge, J.L.5    Landsman, D.6
  • 13
    • 0037396807 scopus 로고    scopus 로고
    • Computationally identifying novel NF-kappa B-regulated immune genes in the human genome
    • Liu,R., McEachin,R.C. and States,D.J. (2003) Computationally identifying novel NF-kappa B-regulated immune genes in the human genome. Genome Res., 13, 654-661.
    • (2003) Genome Res. , vol.13 , pp. 654-661
    • Liu, R.1    McEachin, R.C.2    States, D.J.3
  • 15
    • 0037386472 scopus 로고    scopus 로고
    • An approach to identify over-represented cis-elements in related sequences
    • Zheng,J., Wu,J. and Sun,Z. (2003) An approach to identify over-represented cis-elements in related sequences. Nucleic Acids Res., 31, 1995-2005.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 1995-2005
    • Zheng, J.1    Wu, J.2    Sun, Z.3
  • 16
    • 0038444122 scopus 로고    scopus 로고
    • Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells
    • Elkon,R., Linhart,C., Sharan,R., Shamir,R. and Shiloh,Y. (2003) Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells. Genome Res., 13, 773-780.
    • (2003) Genome Res. , vol.13 , pp. 773-780
    • Elkon, R.1    Linhart, C.2    Sharan, R.3    Shamir, R.4    Shiloh, Y.5
  • 17
    • 1242326890 scopus 로고    scopus 로고
    • CREME: A framework for identifying cis-regulatory modules in human-mouse conserved segments
    • Sharan,R., Ovcharenko,I., Ben-Hur,A. and Karp,R.M. (2003) CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments. Bioinformatics, 19 (Suppl. 1), I283-I291.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 1
    • Sharan, R.1    Ovcharenko, I.2    Ben-Hur, A.3    Karp, R.M.4
  • 18
  • 19
    • 0028685490 scopus 로고
    • Fitting a mixture model by expectation maximization to discover motifs in biopolymers
    • Bailey,T.L. and Elkan,C. (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol., 2, 28-36.
    • (1994) Proc. Int. Conf. Intell. Syst. Mol. Biol. , vol.2 , pp. 28-36
    • Bailey, T.L.1    Elkan, C.2
  • 20
    • 0031787969 scopus 로고    scopus 로고
    • Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation
    • Roth,F.P., Hughes,J.D., Estep,P.W. and Church,G.M. (1998) Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat. Biotechnol., 16, 939-945.
    • (1998) Nat. Biotechnol. , vol.16 , pp. 939-945
    • Roth, F.P.1    Hughes, J.D.2    Estep, P.W.3    Church, G.M.4
  • 21
    • 0031855197 scopus 로고    scopus 로고
    • Automatic extraction of motifs represented in the hidden Markov model from a number of DNA sequences
    • Yada,T., Totoki,Y., Ishikawa,M., Asai,K. and Nakai,K. (1998) Automatic extraction of motifs represented in the hidden Markov model from a number of DNA sequences. Bioinformatics, 14, 317-325.
    • (1998) Bioinformatics , vol.14 , pp. 317-325
    • Yada, T.1    Totoki, Y.2    Ishikawa, M.3    Asai, K.4    Nakai, K.5
  • 22
    • 0032826179 scopus 로고    scopus 로고
    • Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
    • Hertz,G.Z. and Stormo,G.D. (1999) Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics, 15, 563-577.
    • (1999) Bioinformatics , vol.15 , pp. 563-577
    • Hertz, G.Z.1    Stormo, G.D.2
  • 23
    • 0033376806 scopus 로고    scopus 로고
    • Local multiple sequence alignment using dead-end elimination
    • Lukashin,A.V. and Rosa,J.J. (1999) Local multiple sequence alignment using dead-end elimination. Bioinformatics, 15, 947-953.
    • (1999) Bioinformatics , vol.15 , pp. 947-953
    • Lukashin, A.V.1    Rosa, J.J.2
  • 25
    • 0034628901 scopus 로고    scopus 로고
    • Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae
    • Hughes,J.D., Estep,P.W., Tavazoie,S. and Church,G.M. (2000) Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J. Mol. Biol., 296, 1205-1214.
    • (2000) J. Mol. Biol. , vol.296 , pp. 1205-1214
    • Hughes, J.D.1    Estep, P.W.2    Tavazoie, S.3    Church, G.M.4
  • 26
    • 0035187203 scopus 로고    scopus 로고
    • Combining frequency and positional information to predict transcription factor binding sites
    • Kielbasa,S.M., Korbel,J.O., Beule,D., Schuchhardt,J. and Herzel,H. (2001) Combining frequency and positional information to predict transcription factor binding sites. Bioinformatics, 17, 1019-1026.
    • (2001) Bioinformatics , vol.17 , pp. 1019-1026
    • Kielbasa, S.M.1    Korbel, J.O.2    Beule, D.3    Schuchhardt, J.4    Herzel, H.5
  • 27
    • 0035228215 scopus 로고    scopus 로고
    • BioProspector: Discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes
    • Liu,X., Brutlag,D.L. and Liu,J.S. (2001) BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac. Symp. Biocomput., 127-138.
    • (2001) Pac. Symp. Biocomput. , pp. 127-138
    • Liu, X.1    Brutlag, D.L.2    Liu, J.S.3
  • 28
    • 0036137323 scopus 로고    scopus 로고
    • A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling
    • Thijs,G., Lescot,M., Marchal,K., Rombauts,S., De Moor,B., Rouze,P. and Moreau,Y. (2001) A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling. Bioinformatics, 17, 1113-1122.
    • (2001) Bioinformatics , vol.17 , pp. 1113-1122
    • Thijs, G.1    Lescot, M.2    Marchal, K.3    Rombauts, S.4    De Moor, B.5    Rouze, P.6    Moreau, Y.7
  • 29
    • 0034808877 scopus 로고    scopus 로고
    • Tsukuba BB: A branch and bound algorithm for local multiple alignment of DNA and protein sequences
    • Horton,P. (2001) Tsukuba BB: a branch and bound algorithm for local multiple alignment of DNA and protein sequences. J. Comput. Biol., 8, 283-303.
    • (2001) J. Comput. Biol. , vol.8 , pp. 283-303
    • Horton, P.1
  • 30
    • 0036772332 scopus 로고    scopus 로고
    • Finding motifs in the twilight zone
    • Keich,U. and Pevzner,P.A. (2002) Finding motifs in the twilight zone. Bioinformatics, 18, 1374-1381.
    • (2002) Bioinformatics , vol.18 , pp. 1374-1381
    • Keich, U.1    Pevzner, P.A.2
  • 31
    • 0036110853 scopus 로고    scopus 로고
    • Finding motifs using random projections
    • Buhler,J. and Tompa,M. (2002) Finding motifs using random projections. J. Comput. Biol., 9, 225-242.
    • (2002) J. Comput. Biol. , vol.9 , pp. 225-242
    • Buhler, J.1    Tompa, M.2
  • 32
    • 1242264319 scopus 로고    scopus 로고
    • Finding functional sequence elements by multiple local alignment
    • Frith,M.C., Hansen,U., Spouge,J.L. and Weng,Z. (2004) Finding functional sequence elements by multiple local alignment. Nucleic Acids Res., 32, 189-200.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 189-200
    • Frith, M.C.1    Hansen, U.2    Spouge, J.L.3    Weng, Z.4
  • 33
    • 0347075563 scopus 로고    scopus 로고
    • Correlating gene promoters and expression in gene disruption experiments
    • Palin,K., Ukkonen,E., Brazma,A. and Vilo,J. (2002) Correlating gene promoters and expression in gene disruption experiments. Bioinformatics, 18 (Suppl. 2), S172-180.
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 2
    • Palin, K.1    Ukkonen, E.2    Brazma, A.3    Vilo, J.4
  • 34
    • 0034821699 scopus 로고    scopus 로고
    • Cis element/transcription factor analysis (cis/TF): A method for discovering transcription factor/cis element relationships
    • Birnbaum,K., Benfey,P.N. and Shasha,D.E. (2001) cis element/transcription factor analysis (cis/TF): a method for discovering transcription factor/cis element relationships. Genome Res., 11, 1567-1573.
    • (2001) Genome Res. , vol.11 , pp. 1567-1573
    • Birnbaum, K.1    Benfey, P.N.2    Shasha, D.E.3
  • 35
    • 0036300823 scopus 로고    scopus 로고
    • Computational identification of transcription factor binding sites via a transcription-factor-centric clustering (TFCC) algorithm
    • Zhu,Z., Pilpel,Y. and Church,G.M. (2002) Computational identification of transcription factor binding sites via a transcription-factor-centric clustering (TFCC) algorithm. J. Mol. Biol., 318, 71-81.
    • (2002) J. Mol. Biol. , vol.318 , pp. 71-81
    • Zhu, Z.1    Pilpel, Y.2    Church, G.M.3
  • 38
    • 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
  • 42
    • 0002759539 scopus 로고
    • Unsupervised learning of multiple motifs in biopolymers using expectation maximization
    • Bailey,T.L. and Elkan,C. (1995) Unsupervised learning of multiple motifs in biopolymers using expectation maximization. Machine Learning, 21, 51-80.
    • (1995) Machine Learning , vol.21 , pp. 51-80
    • Bailey, T.L.1    Elkan, C.2
  • 45
    • 0031427079 scopus 로고    scopus 로고
    • The phosphatase system in Saccharomyces cerevisiae
    • Oshima,Y. (1997) The phosphatase system in Saccharomyces cerevisiae. Genes Genet. Syst., 72, 323-334.
    • (1997) Genes Genet. Syst. , vol.72 , pp. 323-334
    • Oshima, Y.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.