메뉴 건너뛰기




Volumn 17, Issue 12, 2007, Pages 1919-1931

Reliable prediction of regulator targets using 12 Drosophila genomes

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; TRANSCRIPTION FACTOR;

EID: 38849171836     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.7090407     Document Type: Article
Times cited : (136)

References (73)
  • 1
    • 21644470638 scopus 로고    scopus 로고
    • CrebA regulates secretory activity in the Drosophila salivary gland and epidermis
    • Abrams, E.W. and Andrew, D.J. 2005. CrebA regulates secretory activity in the Drosophila salivary gland and epidermis. Development 132: 2743-2758.
    • (2005) Development , vol.132 , pp. 2743-2758
    • Abrams, E.W.1    Andrew, D.J.2
  • 2
    • 33745586053 scopus 로고    scopus 로고
    • FlyTF: A systematic review of site-specific transcription factors in the fruit fly Drosophila melanogaster
    • Adryan, B. and Teichmann, S.A. 2006. FlyTF: A systematic review of site-specific transcription factors in the fruit fly Drosophila melanogaster. Bioinformatics 22: 1532-1533.
    • (2006) Bioinformatics , vol.22 , pp. 1532-1533
    • Adryan, B.1    Teichmann, S.A.2
  • 4
    • 0028973380 scopus 로고
    • Suppressor of hairless directly activates transcription of enhancer of split complex genes in response to Notch receptor activity
    • Bailey, A.M. and Posakony, J.W. 1995. Suppressor of hairless directly activates transcription of enhancer of split complex genes in response to Notch receptor activity. Genes & Dev. 9: 2609-2622.
    • (1995) Genes & Dev , vol.9 , pp. 2609-2622
    • Bailey, A.M.1    Posakony, J.W.2
  • 5
    • 17444402501 scopus 로고    scopus 로고
    • Drosophila DNase I footprint database: A systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster
    • Bergman, C.M., Carlson, J.W., and Celniker, S.E. 2005. Drosophila DNase I footprint database: A systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster. Bioinformatics 21: 1747-1749.
    • (2005) Bioinformatics , vol.21 , pp. 1747-1749
    • Bergman, C.M.1    Carlson, J.W.2    Celniker, S.E.3
  • 6
    • 0037154273 scopus 로고    scopus 로고
    • Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome
    • Berman, B.P., Nibu, Y., Pfeiffer, B.D., Tomancak, P., Celniker, S.E., Levine, M., Rubin, G.M., and Eisen, M.B. 2002. Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc. Natl. Acad. Sci. 99: 757-762.
    • (2002) Proc. Natl. Acad. Sci , vol.99 , pp. 757-762
    • Berman, B.P.1    Nibu, Y.2    Pfeiffer, B.D.3    Tomancak, P.4    Celniker, S.E.5    Levine, M.6    Rubin, G.M.7    Eisen, M.B.8
  • 8
    • 11944253901 scopus 로고    scopus 로고
    • Cambridge University Press, Cambridge, UK
    • Bollobás, B. 2001. Random graphs. Cambridge University Press, Cambridge, UK.
    • (2001) Random graphs
    • Bollobás, B.1
  • 10
    • 18044377963 scopus 로고    scopus 로고
    • Principles of microRNA-target recognition
    • doi: 10.1371/journal.pbio.0030085
    • Brennecke, J., Stark, A., Russell, R.B., and Cohen, S.M. 2005. Principles of microRNA-target recognition. PLoS Biol. 3: e85. doi: 10.1371/journal.pbio.0030085.
    • (2005) PLoS Biol , vol.3
    • Brennecke, J.1    Stark, A.2    Russell, R.B.3    Cohen, S.M.4
  • 11
    • 55449121696 scopus 로고    scopus 로고
    • Revealing posttranscriptional regulatory elements through network-level conservation
    • doi: 10.1371/journal.pcbi.0010069
    • Chan, C.S., Elemento, O., and Tavazoie, S. 2005. Revealing posttranscriptional regulatory elements through network-level conservation. PLoS Comput. Biol. 1: e69. doi: 10.1371/journal.pcbi.0010069.
    • (2005) PLoS Comput. Biol , vol.1
    • Chan, C.S.1    Elemento, O.2    Tavazoie, S.3
  • 14
    • 32444446240 scopus 로고    scopus 로고
    • Gene regulatory networks and the evolution of animal body plans
    • Davidson, E.H. and Erwin, D.H. 2006. Gene regulatory networks and the evolution of animal body plans. Science 311: 796-800.
    • (2006) Science , vol.311 , pp. 796-800
    • Davidson, E.H.1    Erwin, D.H.2
  • 16
    • 47149117454 scopus 로고    scopus 로고
    • Evolution of genes and genomes on the Drosophila phylogeny
    • Drosophila 12 Genomes Consortium, in press doi: 10.1038/nature06341
    • Drosophila 12 Genomes Consortium. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature (in press) doi: 10.1038/nature06341.
    • (2007) Nature
  • 17
    • 14644390333 scopus 로고    scopus 로고
    • A model of the statistical power of comparative genome sequence analysis
    • doi: 10.1371/journal.pbio. 0030010
    • Eddy, S.R. 2005. A model of the statistical power of comparative genome sequence analysis. PLoS Biol. 3: e10. doi: 10.1371/journal.pbio. 0030010.
    • (2005) PLoS Biol , vol.3
    • Eddy, S.R.1
  • 19
    • 33744507263 scopus 로고    scopus 로고
    • The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates
    • doi: 10.1186/gb-2005-6-12-r104
    • Ettwiller, L., Paten, B., Souren, M., Loosli, F., Wittbrodt, J., and Birney, E. 2005. The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates. Genome Biol. 6: R104. doi: 10.1186/gb-2005-6-12-r104.
    • (2005) Genome Biol , vol.6
    • Ettwiller, L.1    Paten, B.2    Souren, M.3    Loosli, F.4    Wittbrodt, J.5    Birney, E.6
  • 22
    • 27344456287 scopus 로고    scopus 로고
    • microRNA target predictions across seven Drosophila species and comparison to mammalian targets
    • doi: 10.1371/journal.pcbi.0010013
    • Grun, D., Wang, Y.L., Langenberger, D., Gunsalus, K.C., and Rajewsky, N. 2005. microRNA target predictions across seven Drosophila species and comparison to mammalian targets. PLoS Comput. Biol. 1: e13. doi: 10.1371/journal.pcbi.0010013.
    • (2005) PLoS Comput. Biol , vol.1
    • Grun, D.1    Wang, Y.L.2    Langenberger, D.3    Gunsalus, K.C.4    Rajewsky, N.5
  • 24
    • 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
  • 26
    • 0025981572 scopus 로고
    • Spatial regulation of the gap gene giant during Drosophila development
    • Kraut, R. and Levine, M. 1991. Spatial regulation of the gap gene giant during Drosophila development. Development 111: 601-609.
    • (1991) Development , vol.111 , pp. 601-609
    • Kraut, R.1    Levine, M.2
  • 27
    • 19544390155 scopus 로고    scopus 로고
    • Predicting and validating microRNA targets
    • doi: 10.1186/gb-2004-5-9-115
    • Lai, E.C. 2004. Predicting and validating microRNA targets. Genome Biol. 5: 115. doi: 10.1186/gb-2004-5-9-115.
    • (2004) Genome Biol , vol.5 , pp. 115
    • Lai, E.C.1
  • 28
    • 0031767514 scopus 로고    scopus 로고
    • The K box, a conserved 3′ UTR sequence motif, negatively regulates accumulation of enhancer of split complex transcripts
    • Lai, E.C., Burks, C., and Posakony, J.W. 1998. The K box, a conserved 3′ UTR sequence motif, negatively regulates accumulation of enhancer of split complex transcripts. Development 125: 4077-4088.
    • (1998) Development , vol.125 , pp. 4077-4088
    • Lai, E.C.1    Burks, C.2    Posakony, J.W.3
  • 31
    • 0034598832 scopus 로고    scopus 로고
    • Evidence for stabilizing selection in a eukaryotic enhancer element
    • Ludwig, M.Z., Bergman, C., Patel, N.H., and Kreitman, M. 2000. Evidence for stabilizing selection in a eukaryotic enhancer element. Nature 403: 564-567.
    • (2000) Nature , vol.403 , pp. 564-567
    • Ludwig, M.Z.1    Bergman, C.2    Patel, N.H.3    Kreitman, M.4
  • 33
    • 10744222156 scopus 로고    scopus 로고
    • Identification and characterization of multi-species conserved sequences
    • Margulies, E.H., Blanchette, M., Haussler, D., and Green, E.D. 2003. Identification and characterization of multi-species conserved sequences. Genome Res. 13: 2507-2518.
    • (2003) Genome Res , vol.13 , pp. 2507-2518
    • Margulies, E.H.1    Blanchette, M.2    Haussler, D.3    Green, E.D.4
  • 37
  • 39
    • 22144491990 scopus 로고    scopus 로고
    • MONKEY: Identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model
    • doi: 10.1186/gb-2004-5-12-r98
    • Moses, A.M., Chiang, D.Y., Pollard, D.A., Iyer, V.N., and Eisen, M.B. 2004. MONKEY: Identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model. Genome Biol. 5: R98. doi: 10.1186/gb-2004-5-12-r98.
    • (2004) Genome Biol , vol.5
    • Moses, A.M.1    Chiang, D.Y.2    Pollard, D.A.3    Iyer, V.N.4    Eisen, M.B.5
  • 40
  • 41
    • 33845650208 scopus 로고    scopus 로고
    • A graph-based motif detection algorithm models complex nucleotide dependencies in transcription factor binding sites
    • doi: 10.1093/nar/gkl585
    • Naughton, B.T., Fratkin, E., Batzoglou, S., and Brutlag, D.L. 2006. A graph-based motif detection algorithm models complex nucleotide dependencies in transcription factor binding sites. Nucleic Acids Res. 34: 5730-5739. doi: 10.1093/nar/gkl585.
    • (2006) Nucleic Acids Res , vol.34 , pp. 5730-5739
    • Naughton, B.T.1    Fratkin, E.2    Batzoglou, S.3    Brutlag, D.L.4
  • 42
    • 33646930634 scopus 로고    scopus 로고
    • Expression-guided in silico evaluation of candidate cis regulatory codes for Drosophila muscle founder cells
    • doi: 10.1371/journal.pcbi.0020053
    • Philippakis, A.A., Busser, B.W., Gisselbrecht, S.S., He, F.S., Estrada, B., Michelson, A.M., and Bulyk, M.L. 2006. Expression-guided in silico evaluation of candidate cis regulatory codes for Drosophila muscle founder cells. PLoS Comput. Biol. 2: e53. doi: 10.1371/journal.pcbi.0020053.
    • (2006) PLoS Comput. Biol , vol.2
    • Philippakis, A.A.1    Busser, B.W.2    Gisselbrecht, S.S.3    He, F.S.4    Estrada, B.5    Michelson, A.M.6    Bulyk, M.L.7
  • 43
    • 0029789461 scopus 로고    scopus 로고
    • Searching databases of conserved sequence regions by aligning protein multiple-alignments
    • Pietrokovski, S. 1996. Searching databases of conserved sequence regions by aligning protein multiple-alignments. Nucleic Acids Res. 24: 3836-3846.
    • (1996) Nucleic Acids Res , vol.24 , pp. 3836-3846
    • Pietrokovski, S.1
  • 45
    • 33745248430 scopus 로고    scopus 로고
    • MicroRNA target predictions in animals
    • Rajewsky, N. 2006. MicroRNA target predictions in animals. Nat. Genet. 38: S8-S13.
    • (2006) Nat. Genet , vol.38
    • Rajewsky, N.1
  • 47
    • 0347125328 scopus 로고    scopus 로고
    • JASPAR: An open-access database for eukaryotic transcription factor binding profiles
    • doi: 10.1093/nar/gkh012
    • Sandelin, A., Alkema, W., Engstrom, P., Wasserman, W.W., and Lenhard, B. 2004. JASPAR: An open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res. 32: D91-D94. doi: 10.1093/nar/gkh012.
    • (2004) Nucleic Acids Res , vol.32
    • Sandelin, A.1    Alkema, W.2    Engstrom, P.3    Wasserman, W.W.4    Lenhard, B.5
  • 48
    • 33847271755 scopus 로고    scopus 로고
    • A core transcriptional network for early mesoderm development in Drosophila melanogaster
    • Sandmann, T., Girardot, C., Brehme, M., Tongprasit, W., Stolc, V., and Furlong, E.E. 2007. A core transcriptional network for early mesoderm development in Drosophila melanogaster. Genes & Dev. 21: 436-449.
    • (2007) Genes & Dev , vol.21 , pp. 436-449
    • Sandmann, T.1    Girardot, C.2    Brehme, M.3    Tongprasit, W.4    Stolc, V.5    Furlong, E.E.6
  • 49
    • 33646858607 scopus 로고    scopus 로고
    • A temporal map of transcription factor activity: Mef2 directly regulates target genes at all stages of muscle development
    • Sandmann, T., Jensen, L.J., Jakobsen, J.S., Karzynski, M.M., Eichenlaub, M.P., Bork, P., and Furlong, E.E. 2006. A temporal map of transcription factor activity: mef2 directly regulates target genes at all stages of muscle development. Dev. Cell 10: 797-807.
    • (2006) Dev. Cell , vol.10 , pp. 797-807
    • Sandmann, T.1    Jensen, L.J.2    Jakobsen, J.S.3    Karzynski, M.M.4    Eichenlaub, M.P.5    Bork, P.6    Furlong, E.E.7
  • 50
    • 13844275301 scopus 로고    scopus 로고
    • Similarity of position frequency matrices for transcription factor binding sites
    • Schones, D.E., Sumazin, P., and Zhang, M.Q. 2005. Similarity of position frequency matrices for transcription factor binding sites. Bioinformatics 21: 307-313.
    • (2005) Bioinformatics , vol.21 , pp. 307-313
    • Schones, D.E.1    Sumazin, P.2    Zhang, M.Q.3
  • 52
    • 31044444975 scopus 로고    scopus 로고
    • TarBase: A comprehensive database of experimentally supported animal microRNA targets
    • Sethupathy, P., Corda, B., and Hatzigeorgiou, A.G. 2006. TarBase: A comprehensive database of experimentally supported animal microRNA targets. RNA 12: 192-197.
    • (2006) RNA , vol.12 , pp. 192-197
    • Sethupathy, P.1    Corda, B.2    Hatzigeorgiou, A.G.3
  • 55
    • 4243170045 scopus 로고    scopus 로고
    • Identification of Drosophila microRNA targets
    • doi: 10.1371/journal.pbio.0000060
    • Stark, A., Brennecke, J., Russell, R.B., and Cohen, S.M. 2003. Identification of Drosophila microRNA targets. PLoS Biol. 1: e60. doi: 10.1371/journal.pbio.0000060.
    • (2003) PLoS Biol , vol.1
    • Stark, A.1    Brennecke, J.2    Russell, R.B.3    Cohen, S.M.4
  • 56
    • 28944439309 scopus 로고    scopus 로고
    • Animal MicroRNAs confer robustness to gene expression and have a significant impact on 3UTR evolution
    • Stark, A., Brennecke, J., Bushati, N., Russell, R.B., and Cohen, S.M. 2005. Animal MicroRNAs confer robustness to gene expression and have a significant impact on 3UTR evolution. Cell 123: 1133-1146.
    • (2005) Cell , vol.123 , pp. 1133-1146
    • Stark, A.1    Brennecke, J.2    Bushati, N.3    Russell, R.B.4    Cohen, S.M.5
  • 58
    • 0034072450 scopus 로고    scopus 로고
    • DNA binding sites: Representation and discovery
    • Stormo, G.D. 2000. DNA binding sites: Representation and discovery. Bioinformatics 16: 16-23.
    • (2000) Bioinformatics , vol.16 , pp. 16-23
    • Stormo, G.D.1
  • 59
    • 33845303175 scopus 로고    scopus 로고
    • ESPERR: Learning strong and weak signals in genomic sequence alignments to identify functional elements
    • Taylor, J., Tyekucheva, S., King, D.C., Hardison, R.C., Miller, W., and Chiaromonte, F. 2006. ESPERR: Learning strong and weak signals in genomic sequence alignments to identify functional elements. Genome Res. 16: 1596-1604.
    • (2006) Genome Res , vol.16 , pp. 1596-1604
    • Taylor, J.1    Tyekucheva, S.2    King, D.C.3    Hardison, R.C.4    Miller, W.5    Chiaromonte, F.6
  • 63
    • 0025194307 scopus 로고
    • Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase
    • Tuerk, C. and Gold, L. 1990. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249: 505-510.
    • (1990) Science , vol.249 , pp. 505-510
    • Tuerk, C.1    Gold, L.2
  • 64
    • 0037380723 scopus 로고    scopus 로고
    • Comparative genomics: Genome-wide analysis in metazoan eukaryotes
    • Ureta-Vidal, A., Ettwiller, L., and Birney, E. 2003. Comparative genomics: Genome-wide analysis in metazoan eukaryotes. Nat. Rev. Genet. 4: 251-262.
    • (2003) Nat. Rev. Genet , vol.4 , pp. 251-262
    • Ureta-Vidal, A.1    Ettwiller, L.2    Birney, E.3
  • 65
    • 0028034321 scopus 로고
    • Negative regulation of proneural gene activity: Hairy is a direct transcriptional repressor of achaete
    • Van Doren, M., Bailey, A.M., Esnayra, J., Ede, K., and Posakony, J.W. 1994. Negative regulation of proneural gene activity: hairy is a direct transcriptional repressor of achaete. Genes & Dev. 8: 2729-2742.
    • (1994) Genes & Dev , vol.8 , pp. 2729-2742
    • Van Doren, M.1    Bailey, A.M.2    Esnayra, J.3    Ede, K.4    Posakony, J.W.5
  • 66
    • 1842584947 scopus 로고    scopus 로고
    • Applied bioinformatics for the identification of regulatory elements
    • Wasserman, W.W. and Sandelin, A. 2004. Applied bioinformatics for the identification of regulatory elements. Nat. Rev. Genet. 5: 276-287.
    • (2004) Nat. Rev. Genet , vol.5 , pp. 276-287
    • Wasserman, W.W.1    Sandelin, A.2
  • 69
    • 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., Kulbokas, 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    Kulbokas, E.J.3    Golub, T.R.4    Mootha, V.5    Lindblad-Toh, K.6    Lander, E.S.7    Kellis, M.8
  • 70
    • 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
  • 71
    • 0031805714 scopus 로고    scopus 로고
    • Regulation and function of tinman during dorsal mesoderm induction and heart specification in Drosophila
    • Yin, Z. and Frasch, M. 1998. Regulation and function of tinman during dorsal mesoderm induction and heart specification in Drosophila. Dev. Genet. 22: 187-200.
    • (1998) Dev. Genet , vol.22 , pp. 187-200
    • Yin, Z.1    Frasch, M.2
  • 72
    • 33847189172 scopus 로고    scopus 로고
    • Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo
    • Zeitlinger, J., Zinzen, R.P., Stark, A., Kellis, M., Zhang, H., Young, R.A., and Levine, M. 2007. Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo. Genes & Dev. 21: 385-390.
    • (2007) Genes & Dev , vol.21 , pp. 385-390
    • Zeitlinger, J.1    Zinzen, R.P.2    Stark, A.3    Kellis, M.4    Zhang, H.5    Young, R.A.6    Levine, M.7
  • 73
    • 4344607122 scopus 로고    scopus 로고
    • CisModule: De novo discovery of cis-regulatory modules by hierarchical mixture modeling
    • Zhou, Q. and Wong, W.H. 2004. CisModule: De novo discovery of cis-regulatory modules by hierarchical mixture modeling. Proc. Natl. Acad. Sci. 101: 12114-12119.
    • (2004) Proc. Natl. Acad. Sci , vol.101 , pp. 12114-12119
    • Zhou, Q.1    Wong, W.H.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.