메뉴 건너뛰기




Volumn 16, Issue 12, 2006, Pages 1445-1454

Unraveling transcription regulatory networks by protein-DNA and protein-protein interaction mapping

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBONUCLEOPROTEIN;

EID: 33845311536     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.5321506     Document Type: Review
Times cited : (130)

References (87)
  • 2
    • 0034721164 scopus 로고    scopus 로고
    • Error and attack tolerance of complex networks
    • Albert, R., Jeong, H., and Barabasi, A.-L. 2000. Error and attack tolerance of complex networks. Nature 378: 378-381.
    • (2000) Nature , vol.378 , pp. 378-381
    • Albert, R.1    Jeong, H.2    Barabasi, A.-L.3
  • 3
    • 4644309196 scopus 로고    scopus 로고
    • The functions of animal microRNAs
    • Ambros, V. 2004. The functions of animal microRNAs. Nature 431: 350-355.
    • (2004) Nature , vol.431 , pp. 350-355
    • Ambros, V.1
  • 5
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: Understanding the cell's functional organization
    • Barabasi, A.L. and Oltvai, Z.N. 2004. Network biology: Understanding the cell's functional organization. Nat. Rev. Genet. 5: 101-113.
    • (2004) Nat. Rev. Genet. , vol.5 , pp. 101-113
    • Barabasi, A.L.1    Oltvai, Z.N.2
  • 9
    • 33745140886 scopus 로고    scopus 로고
    • Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome
    • Bieda, M., Xu, X., Singer, M.A., Green, R., and Farnham, P.J. 2006. Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome. Genome Res. 16: 595-605.
    • (2006) Genome Res. , vol.16 , pp. 595-605
    • Bieda, M.1    Xu, X.2    Singer, M.A.3    Green, R.4    Farnham, P.J.5
  • 10
    • 22344449669 scopus 로고    scopus 로고
    • Constructing transcriptional regulatory networks
    • Blais, A. and Dynlacht, B.D. 2005. Constructing transcriptional regulatory networks. Genes & Dev. 19: 1499-1511.
    • (2005) Genes & Dev. , vol.19 , pp. 1499-1511
    • Blais, A.1    Dynlacht, B.D.2
  • 16
    • 10744226888 scopus 로고    scopus 로고
    • Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs
    • Cawley, S., Bekiranov, S., Ng, H.H., Kapranov, P., Sekinger, E.A., Kampa, D., Piccolboni, A., Sementchenko, V., Cheng, J., Williams, A.J., et al. 2004. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116: 499-509.
    • (2004) Cell , vol.116 , pp. 499-509
    • Cawley, S.1    Bekiranov, S.2    Ng, H.H.3    Kapranov, P.4    Sekinger, E.A.5    Kampa, D.6    Piccolboni, A.7    Sementchenko, V.8    Cheng, J.9    Williams, A.J.10
  • 19
    • 30044451918 scopus 로고    scopus 로고
    • Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome
    • Cooper, S.J., Trinklein, N.D., Anton, E.D., Nguyen, L., and Myers, R.M. 2006. Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome. Genome Res. 16: 1-10.
    • (2006) Genome Res. , vol.16 , pp. 1-10
    • Cooper, S.J.1    Trinklein, N.D.2    Anton, E.D.3    Nguyen, L.4    Myers, R.M.5
  • 24
  • 26
    • 0030669030 scopus 로고    scopus 로고
    • Exploring the metabolic and genetic control of gene expression on a genomic scale
    • DeRisi, J.L., Iyer, V., 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.2    Brown, P.O.3
  • 28
    • 28044455435 scopus 로고    scopus 로고
    • MicroPrimer: The biogenesis and function of microRNA
    • Du, T. and Zamore, P.D. 2005. microPrimer: The biogenesis and function of microRNA. Development 132: 4645-4652.
    • (2005) Development , vol.132 , pp. 4645-4652
    • Du, T.1    Zamore, P.D.2
  • 30
    • 33845341455 scopus 로고    scopus 로고
    • Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques
    • Elnitski, L., Jin, V.X., Farnham, P.J., and Jones, S.J.M. 2006. Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques. Genome Res. (this issue).
    • (2006) Genome Res. , Issue.THIS ISSUE
    • Elnitski, L.1    Jin, V.X.2    Farnham, P.J.3    Jones, S.J.M.4
  • 31
    • 7444260846 scopus 로고    scopus 로고
    • The ENCODE (ENCyclopedia of DNA elements) project
    • ENCODE Project Consortium
    • ENCODE Project Consortium. 2004. The ENCODE (ENCyclopedia of DNA elements) project. Science 306: 636-640.
    • (2004) Science , vol.306 , pp. 636-640
  • 32
    • 0024406857 scopus 로고
    • A novel genetic system to detect protein-protein interactions
    • Fields, S. and Song, O. 1989. A novel genetic system to detect protein-protein interactions. Nature 340: 245-246.
    • (1989) Nature , vol.340 , pp. 245-246
    • Fields, S.1    Song, O.2
  • 34
    • 22344454794 scopus 로고    scopus 로고
    • Ultraconserved elements in insect genomes: A highly conserved intronic sequence implicated in the control of homothorax mRNA splicing
    • Glazov, E.A., Pheasant, M., McGraw, E.A., Bejerano, G., and Mattick, J.S. 2005. Ultraconserved elements in insect genomes: A highly conserved intronic sequence implicated in the control of homothorax mRNA splicing. Genome Res. 15: 800-808.
    • (2005) Genome Res. , vol.15 , pp. 800-808
    • Glazov, E.A.1    Pheasant, M.2    McGraw, E.A.3    Bejerano, G.4    Mattick, J.S.5
  • 36
    • 0036578654 scopus 로고    scopus 로고
    • Topological and causal structure of the yeast transcriptional regulatory network
    • Guelzim, N., Bottani, S., Bourgine, P., and Kepes, F. 2002. Topological and causal structure of the yeast transcriptional regulatory network. Nat. Genet. 31: 60-63.
    • (2002) Nat. Genet. , vol.31 , pp. 60-63
    • Guelzim, N.1    Bottani, S.2    Bourgine, P.3    Kepes, F.4
  • 37
    • 18844396103 scopus 로고    scopus 로고
    • De novo cis-regulatory module elicitation for eukaryotic genomes
    • Gupta, M. and Liu, J.S. 2005. De novo cis-regulatory module elicitation for eukaryotic genomes. Proc. Natl. Acad. Sci. 102: 7079-7084.
    • (2005) Proc. Natl. Acad. Sci. , vol.102 , pp. 7079-7084
    • Gupta, M.1    Liu, J.S.2
  • 38
    • 5644229499 scopus 로고    scopus 로고
    • Regulation of gene expression by a metabolic enzyme
    • Hall, D.A., Zhu, H., Zhu, X., Royce, T., Gerstein, M., and Snyder, M. 2004. Regulation of gene expression by a metabolic enzyme. Science 306: 482-484.
    • (2004) Science , vol.306 , pp. 482-484
    • Hall, D.A.1    Zhu, H.2    Zhu, X.3    Royce, T.4    Gerstein, M.5    Snyder, M.6
  • 39
    • 30344439849 scopus 로고    scopus 로고
    • Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity
    • Hallikas, O., Palin, K., Sinjushina, N., Rautiainen, R., Partanen, J., Ukkonen, E., and Taipale, J. 2006. Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity. Cell 124: 47-59.
    • (2006) Cell , vol.124 , pp. 47-59
    • Hallikas, O.1    Palin, K.2    Sinjushina, N.3    Rautiainen, R.4    Partanen, J.5    Ukkonen, E.6    Taipale, J.7
  • 41
    • 0033676098 scopus 로고    scopus 로고
    • DNA cloning using in vitro site-specific recombination
    • Hartley, J.L., Temple, G.F., and Brasch, M.A. 2000. DNA cloning using in vitro site-specific recombination. Genome Res. 10: 1788-1795.
    • (2000) Genome Res. , vol.10 , pp. 1788-1795
    • Hartley, J.L.1    Temple, G.F.2    Brasch, M.A.3
  • 42
    • 10044282898 scopus 로고    scopus 로고
    • A systems view of mRNP biology
    • Hieronymus, H. and Silver, P.A. 2004. A systems view of mRNP biology. Genes & Dev. 18: 2845-2860.
    • (2004) Genes & Dev. , vol.18 , pp. 2845-2860
    • Hieronymus, H.1    Silver, P.A.2
  • 46
    • 0035799707 scopus 로고    scopus 로고
    • Lethality and centrality in protein networks
    • Jeong, H., Mason, S.P., Barabasi, A.-L., and Oltvai, Z.N. 2001. Lethality and centrality in protein networks. Nature 411: 41-42.
    • (2001) Nature , vol.411 , pp. 41-42
    • Jeong, H.1    Mason, S.P.2    Barabasi, A.-L.3    Oltvai, Z.N.4
  • 47
    • 23444446940 scopus 로고    scopus 로고
    • Post-transcriptional operons and regulons co-ordinating gene expression
    • Keene, J.D. and Lager, P.J. 2005. Post-transcriptional operons and regulons co-ordinating gene expression. Chromosome Res. 13: 327-337.
    • (2005) Chromosome Res. , vol.13 , pp. 327-337
    • Keene, J.D.1    Lager, P.J.2
  • 48
    • 0038349948 scopus 로고    scopus 로고
    • Sequencing and comparison of yeast species to identify genes and regulatory elements
    • Kellis, M., Patterson, N., Endrizzi, M., Birren, B., and Lander, E.S. 2003. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423: 241-254.
    • (2003) Nature , vol.423 , pp. 241-254
    • Kellis, M.1    Patterson, N.2    Endrizzi, M.3    Birren, B.4    Lander, E.S.5
  • 52
    • 33644878620 scopus 로고    scopus 로고
    • DBD: A transcription factor prediction database
    • Kummerfeld, S.K. and Teichmann, S.A. 2006. DBD: A transcription factor prediction database. Nucleic Acids Res. 34: D74-D81.
    • (2006) Nucleic Acids Res. , vol.34
    • Kummerfeld, S.K.1    Teichmann, S.A.2
  • 55
    • 0037819447 scopus 로고    scopus 로고
    • Transcription regulation and animal diversity
    • Levine, M. and Tjian, R. 2003. Transcription regulation and animal diversity. Nature 424: 147-151.
    • (2003) Nature , vol.424 , pp. 147-151
    • Levine, M.1    Tjian, R.2
  • 56
    • 0027745644 scopus 로고
    • Isolation of the ORC6, a component of the yeast origin recognition complex by a one-hybrid system
    • Li, J.J. and Herskowitz, I. 1993. Isolation of the ORC6, a component of the yeast origin recognition complex by a one-hybrid system. Science 262: 1870-1874.
    • (1993) Science , vol.262 , pp. 1870-1874
    • Li, J.J.1    Herskowitz, I.2
  • 58
    • 15544375816 scopus 로고    scopus 로고
    • DIP-chip: Rapid and accurate determination of DNA-binding specificity
    • Liu, X., Noll, D.M., Lieb, J.D., and Clarke, N.D. 2005. DIP-chip: Rapid and accurate determination of DNA-binding specificity. Genome Res. 15: 421-427.
    • (2005) Genome Res. , vol.15 , pp. 421-427
    • Liu, X.1    Noll, D.M.2    Lieb, J.D.3    Clarke, N.D.4
  • 59
    • 4644326931 scopus 로고    scopus 로고
    • Genomic analysis of regulatory network dynamics reveals large topological changes
    • Luscombe, N.M., Madan Babu, M., Yu, H., Snyder, M., Teichmann, S.A., and Gerstein, M. 2004. Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431: 308-312.
    • (2004) Nature , vol.431 , pp. 308-312
    • Luscombe, N.M.1    Madan Babu, M.2    Yu, H.3    Snyder, M.4    Teichmann, S.A.5    Gerstein, M.6
  • 61
    • 23444446753 scopus 로고    scopus 로고
    • A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors
    • Meng, X., Brodsky, M.H., and Wolfe, S.A. 2005. A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors. Nat. Biotechnol. 23: 988-994.
    • (2005) Nat. Biotechnol. , vol.23 , pp. 988-994
    • Meng, X.1    Brodsky, M.H.2    Wolfe, S.A.3
  • 64
    • 0037595546 scopus 로고    scopus 로고
    • Comprehensive identification of human bZip interactions with coiled-coil arrays
    • Newman, J.R.S. and Keating, A.E. 2003. Comprehensive identification of human bZip interactions with coiled-coil arrays. Science 300: 2097-2101.
    • (2003) Science , vol.300 , pp. 2097-2101
    • Newman, J.R.S.1    Keating, A.E.2
  • 66
    • 31744438846 scopus 로고    scopus 로고
    • Identification of direct targets of DAF-16 controlling longevity, metabolism and diapause by chromatin immunoprecipitation
    • Oh, S.W., Mukhopadhyay, A., Dixit, B.L., Raha, T., Green, M.R., and Tissenbaum, H.A. 2005. Identification of direct targets of DAF-16 controlling longevity, metabolism and diapause by chromatin immunoprecipitation. Nat. Genet. 38: 251-257.
    • (2005) Nat. Genet. , vol.38 , pp. 251-257
    • Oh, S.W.1    Mukhopadhyay, A.2    Dixit, B.L.3    Raha, T.4    Green, M.R.5    Tissenbaum, H.A.6
  • 68
    • 33744976395 scopus 로고    scopus 로고
    • A compendium of C. elegans regulatory transcription factors: A resource for mapping transcription regulatory networks
    • Reece-Hoyes, J.S., Deplancke, B., Shingles, J., Grove, C.A., Hope, I.A., and Walhout, A.J.M. 2005. A compendium of C. elegans regulatory transcription factors: A resource for mapping transcription regulatory networks. Genome Biol. 6: R110.
    • (2005) Genome Biol. , vol.6
    • Reece-Hoyes, J.S.1    Deplancke, B.2    Shingles, J.3    Grove, C.A.4    Hope, I.A.5    Walhout, A.J.M.6
  • 70
    • 0242467199 scopus 로고    scopus 로고
    • Functional tests of enhancer conservation between distantly related species
    • Ruvinsky, I. and Ruvkun, G. 2003. Functional tests of enhancer conservation between distantly related species. Development 130: 5133-5142.
    • (2003) Development , vol.130 , pp. 5133-5142
    • Ruvinsky, I.1    Ruvkun, G.2
  • 72
    • 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., Boststein, D., Koller, D., and Friedman, N. 2003. Module networks: Identifying regulatory modules and their condition-specific regulators from gene expression data. Nat. Genet. 34: 166-176.
    • (2003) Nat. Genet. , vol.34 , pp. 166-176
    • Segal, E.1    Shapira, M.2    Regev, A.3    Pe'er, D.4    Boststein, D.5    Koller, D.6    Friedman, N.7
  • 74
    • 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: i283-i291.
    • (2003) Bioinformatics , vol.19
    • Sharan, R.1    Ovcharenko, I.2    Ben-Hur, A.3    Karp, R.M.4
  • 75
    • 0036578795 scopus 로고    scopus 로고
    • Network motifs in the transcriptional regulation network of Escherichia coli
    • Shen-Orr, S.S., Milo, R., Mangan, S., and Alon, U. 2002. Network motifs in the transcriptional regulation network of Escherichia coli. Nat. Genet. 31: 64-68.
    • (2002) Nat. Genet. , vol.31 , pp. 64-68
    • Shen-Orr, S.S.1    Milo, R.2    Mangan, S.3    Alon, U.4
  • 79
    • 0034007256 scopus 로고    scopus 로고
    • Identification of in vivo DNA targets of chromatin proteins using tethered Dam methyltransferase
    • van Steensel, B. and Henikoff, S. 2000. Identification of in vivo DNA targets of chromatin proteins using tethered Dam methyltransferase. Nat. Biotechnol. 18: 424-428.
    • (2000) Nat. Biotechnol. , vol.18 , pp. 424-428
    • Van Steensel, B.1    Henikoff, S.2
  • 81
    • 0027213634 scopus 로고
    • Molecular cloning of the olfactory neuronal transcription factor Olf-1 by genetic selection in yeast
    • Wang, M.M. and Reed, R.R. 1993. Molecular cloning of the olfactory neuronal transcription factor Olf-1 by genetic selection in yeast. Nature 364: 121-126.
    • (1993) Nature , vol.364 , pp. 121-126
    • Wang, M.M.1    Reed, R.R.2
  • 84
    • 15244358503 scopus 로고    scopus 로고
    • Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals
    • Xie, X., Lu, J., Kulkobas, E.J., Golub, T.R., Mootha, V., Lindblad-Toh, K., Lander, E.S., and Kellis, M. 2005. Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals. Nature 434: 338-345.
    • (2005) Nature , vol.434 , pp. 338-345
    • Xie, X.1    Lu, J.2    Kulkobas, E.J.3    Golub, T.R.4    Mootha, V.5    Lindblad-Toh, K.6    Lander, E.S.7    Kellis, M.8
  • 85
    • 0042706147 scopus 로고    scopus 로고
    • Genomic analysis of gene expression relationships in transcriptional regulatory networks
    • Yu, H., Luscombe, N.M., Qian, J., and Gerstein, M. 2003. Genomic analysis of gene expression relationships in transcriptional regulatory networks. Trends Genet. 19: 422-427.
    • (2003) Trends Genet. , vol.19 , pp. 422-427
    • Yu, H.1    Luscombe, N.M.2    Qian, J.3    Gerstein, M.4
  • 86
    • 2442477788 scopus 로고    scopus 로고
    • Genomic analysis of essentiality within protein networks
    • Yu, H., Greenbaum, D., Xin Lu, H., Zhu, X., and Gerstein, M. 2004. Genomic analysis of essentiality within protein networks. Trends Genet. 20: 227-231.
    • (2004) Trends Genet. , vol.20 , pp. 227-231
    • Yu, H.1    Greenbaum, D.2    Xin Lu, H.3    Zhu, X.4    Gerstein, M.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.