메뉴 건너뛰기




Volumn 18, Issue 7, 2008, Pages 1180-1189

Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; TRANSCRIPTION FACTOR;

EID: 46449123335     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.076117.108     Document Type: Article
Times cited : (154)

References (41)
  • 1
    • 9144242657 scopus 로고    scopus 로고
    • Comprehensive analysis of the base composition around the transcription start site in Metazoa
    • doi: 10.1186/1471-2164-5-34
    • Aerts, S., Thijs, G., Dabrowski, M., Moreau, Y., and De Moor, B. 2004. Comprehensive analysis of the base composition around the transcription start site in Metazoa. BMC Genomics 5: 34. doi: 10.1186/1471-2164-5-34.
    • (2004) BMC Genomics , vol.5 , pp. 34
    • Aerts, S.1    Thijs, G.2    Dabrowski, M.3    Moreau, Y.4    De Moor, B.5
  • 3
    • 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
  • 7
    • 0037069672 scopus 로고    scopus 로고
    • Large clusters of co-expressed genes in the Drosophila genome
    • Boutanaev, A.M., Kalmykova, A.I., Shevelyov, Y.Y., and Nurminsky, D.I. 2002. Large clusters of co-expressed genes in the Drosophila genome. Nature 420: 666-669.
    • (2002) Nature , vol.420 , pp. 666-669
    • Boutanaev, A.M.1    Kalmykova, A.I.2    Shevelyov, Y.Y.3    Nurminsky, D.I.4
  • 9
    • 0033780450 scopus 로고    scopus 로고
    • A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression
    • Cohen, B.A., Mitra, R.D., Hughes, J.D., and Church, G.M. 2000. A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Nat. Genet. 26: 183-186.
    • (2000) Nat. Genet , vol.26 , pp. 183-186
    • Cohen, B.A.1    Mitra, R.D.2    Hughes, J.D.3    Church, G.M.4
  • 10
    • 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
  • 11
    • 0344376570 scopus 로고    scopus 로고
    • Finding composite regulatory patterns in DNA sequences
    • Eskin, E. and Pevzner, P.A. 2002. Finding composite regulatory patterns in DNA sequences. Bioinformatics 18: S354-S363.
    • (2002) Bioinformatics , vol.18
    • Eskin, E.1    Pevzner, P.A.2
  • 12
    • 34547662962 scopus 로고    scopus 로고
    • Trawler: De novo regulatory motif discovery pipeline for chromatin immunoprecipitation
    • Ettwiller, L., Paten, B., Ramialison, M., Birney, E., and Wittbrodt, J. 2007. Trawler: De novo regulatory motif discovery pipeline for chromatin immunoprecipitation. Nat. Methods 4: 563-565.
    • (2007) Nat. Methods , vol.4 , pp. 563-565
    • Ettwiller, L.1    Paten, B.2    Ramialison, M.3    Birney, E.4    Wittbrodt, J.5
  • 15
    • 0027401676 scopus 로고
    • Characterization of the human ADP-ribosylation factor 3 promoter. Transcriptional regulation of a TATA-less promoter
    • Haun, R.S., Moss, J., and Vaughan, M. 1993. Characterization of the human ADP-ribosylation factor 3 promoter. Transcriptional regulation of a TATA-less promoter. J. Biol. Chem. 268: 8793-8800.
    • (1993) J. Biol. Chem , vol.268 , pp. 8793-8800
    • Haun, R.S.1    Moss, J.2    Vaughan, M.3
  • 16
    • 34547641224 scopus 로고    scopus 로고
    • Genome-wide analyses reveal properties of redundant and specific promoter occupancy within the ETS gene family
    • Hollenhorst, P.C., Shah, A.A., Hopkins, C., and Graves, B.J. 2007. Genome-wide analyses reveal properties of redundant and specific promoter occupancy within the ETS gene family. Genes & Dev. 21: 1882-1894.
    • (2007) Genes & Dev , vol.21 , pp. 1882-1894
    • Hollenhorst, P.C.1    Shah, A.A.2    Hopkins, C.3    Graves, B.J.4
  • 17
    • 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
  • 18
    • 0030710153 scopus 로고    scopus 로고
    • How does DNA methylation repress transcription?
    • Kass, S.U., Pruss, D., and Wolffe, A.P. 1997. How does DNA methylation repress transcription? Trends Genet. 13: 444-449.
    • (1997) Trends Genet , vol.13 , pp. 444-449
    • Kass, S.U.1    Pruss, D.2    Wolffe, A.P.3
  • 21
    • 29244445127 scopus 로고    scopus 로고
    • Deciphering transcriptional regulatory elements that encode specific cell cycle phasing by comparative genomics analysis
    • Linhart, C., Elkon, R., Shiloh, Y., and Shamir, R. 2005. Deciphering transcriptional regulatory elements that encode specific cell cycle phasing by comparative genomics analysis. Cell Cycle 4: 1788-1797.
    • (2005) Cell Cycle , vol.4 , pp. 1788-1797
    • Linhart, C.1    Elkon, R.2    Shiloh, Y.3    Shamir, R.4
  • 22
    • 0034659898 scopus 로고    scopus 로고
    • Genomics, gene expression and DNA arrays
    • Lockhart, D.J. and Winzeler, E.A. 2000. Genomics, gene expression and DNA arrays. Nature 405: 827-836.
    • (2000) Nature , vol.405 , pp. 827-836
    • Lockhart, D.J.1    Winzeler, E.A.2
  • 24
    • 0012253746 scopus 로고    scopus 로고
    • Computational analysis of core promoters in the Drosophila genome
    • doi: 10.1186/gb-2002-3-12-research0087
    • Ohler, U., Liao, G.C., Niemann, H., and Rubin, G.M. 2002. Computational analysis of core promoters in the Drosophila genome. Genome Biol. 3. doi: 10.1186/gb-2002-3-12-research0087.
    • (2002) Genome Biol , vol.3
    • Ohler, U.1    Liao, G.C.2    Niemann, H.3    Rubin, G.M.4
  • 25
    • 0035224579 scopus 로고    scopus 로고
    • An algorithm for finding signals of unknown length in DNA sequences
    • Pavesi, G., Mauri, G., and Pesole, G. 2001. An algorithm for finding signals of unknown length in DNA sequences. Bioinformatics 17: S207-S214.
    • (2001) Bioinformatics , vol.17
    • Pavesi, G.1    Mauri, G.2    Pesole, G.3
  • 26
    • 33845436047 scopus 로고    scopus 로고
    • Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans
    • Ruby, J.G., Jan, C., Player, C., Axtell, M.J., Lee, W., Nusbaum, C., Ge, H., and Bartel, D.P. 2006. Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell 127: 1193-1207.
    • (2006) Cell , vol.127 , pp. 1193-1207
    • Ruby, J.G.1    Jan, C.2    Player, C.3    Axtell, M.J.4    Lee, W.5    Nusbaum, C.6    Ge, H.7    Bartel, D.P.8
  • 28
    • 0037115891 scopus 로고    scopus 로고
    • Discovery of novel transcription factor binding sites by statistical overrepresentation
    • Sinha, S. and Tompa, M. 2002. Discovery of novel transcription factor binding sites by statistical overrepresentation. Nucleic Acids Res. 30: 5549-5560.
    • (2002) Nucleic Acids Res , vol.30 , pp. 5549-5560
    • Sinha, S.1    Tompa, M.2
  • 29
    • 40449124692 scopus 로고    scopus 로고
    • Systematic functional characterization of cis-regulatory motifs in human core promoters
    • Sinha, S., Adler, A.S., Field, Y., Chang, H.Y., and Segal, E. 2008. Systematic functional characterization of cis-regulatory motifs in human core promoters. Genome Res. 18: 477-488.
    • (2008) Genome Res , vol.18 , pp. 477-488
    • Sinha, S.1    Adler, A.S.2    Field, Y.3    Chang, H.Y.4    Segal, E.5
  • 30
    • 0043269205 scopus 로고    scopus 로고
    • The RNA polymerase II core promoter
    • Smale, S.T. and Kadonaga, J.T. 2003. The RNA polymerase II core promoter. Annu. Rev. Biochem. 72: 449-479.
    • (2003) Annu. Rev. Biochem , vol.72 , pp. 449-479
    • Smale, S.T.1    Kadonaga, J.T.2
  • 31
    • 33644499134 scopus 로고    scopus 로고
    • Cell-type-specific signatures of microRNAs on target mRNA expression
    • Sood, P., Krek, A., Zavolan, M., Macino, G., and Rajewsky, N. 2006. Cell-type-specific signatures of microRNAs on target mRNA expression. Proc. Natl. Acad. Sci. 103: 2746-2751.
    • (2006) Proc. Natl. Acad. Sci , vol.103 , pp. 2746-2751
    • Sood, P.1    Krek, A.2    Zavolan, M.3    Macino, G.4    Rajewsky, N.5
  • 32
    • 33746922381 scopus 로고    scopus 로고
    • Tabach, Y., Milyavsky, M., Shats, I., Brosh, R., Zuk, O., Yitzhaky, A., Mantovani, R., Domany, E., Rotter, V., and Pilpel, Y. 2005. The promoters of human cell cycle genes integrate signals from two tumor suppressive pathways during cellular transformation. Mol. Syst. Biol. 1: 2005.0022. doi: 10.1038/msb4100030.
    • Tabach, Y., Milyavsky, M., Shats, I., Brosh, R., Zuk, O., Yitzhaky, A., Mantovani, R., Domany, E., Rotter, V., and Pilpel, Y. 2005. The promoters of human cell cycle genes integrate signals from two tumor suppressive pathways during cellular transformation. Mol. Syst. Biol. 1: 2005.0022. doi: 10.1038/msb4100030.
  • 33
    • 39049163024 scopus 로고    scopus 로고
    • Wide-scale analysis of human functional transcription factor binding reveals a strong bias towards the transcription start site
    • doi: 10.1371/journal.pone.0000807
    • Tabach, Y., Brosh, R., Buganim, Y., Reiner, A., Zuk, O., Yitzhaky, A., Koudritsky, M., Rotter, V., and Domany, E. 2007. Wide-scale analysis of human functional transcription factor binding reveals a strong bias towards the transcription start site. PLoS One 2: e807. doi: 10.1371/journal.pone.0000807.
    • (2007) PLoS One , vol.2
    • Tabach, Y.1    Brosh, R.2    Buganim, Y.3    Reiner, A.4    Zuk, O.5    Yitzhaky, A.6    Koudritsky, M.7    Rotter, V.8    Domany, E.9
  • 35
    • 0035093828 scopus 로고    scopus 로고
    • Chromatin profiling using targeted DNA adenine methyltransferase
    • van Steensel, B., Delrow, J., and Henikoff, S. 2001. Chromatin profiling using targeted DNA adenine methyltransferase. Nat. Genet. 27: 304-308.
    • (2001) Nat. Genet , vol.27 , pp. 304-308
    • van Steensel, B.1    Delrow, J.2    Henikoff, S.3
  • 37
    • 28444493739 scopus 로고    scopus 로고
    • Combining probability from independent tests: The weighted Z-method is superior to Fisher's approach
    • Whitlock, M.C. 2005. Combining probability from independent tests: The weighted Z-method is superior to Fisher's approach. J. Evol. Biol. 18: 1368-1373.
    • (2005) J. Evol. Biol , vol.18 , pp. 1368-1373
    • Whitlock, M.C.1
  • 38
    • 0029960055 scopus 로고    scopus 로고
    • TRANSFAC: A database on transcription factors and their DNA binding sites
    • Wingender, E., Dietze, P., Karas, H., and Knuppel, R. 1996. TRANSFAC: A database on transcription factors and their DNA binding sites. Nucleic Acids Res. 24: 238-241.
    • (1996) Nucleic Acids Res , vol.24 , pp. 238-241
    • Wingender, E.1    Dietze, P.2    Karas, H.3    Knuppel, R.4
  • 39
    • 33746864004 scopus 로고    scopus 로고
    • ChIP-chip comes of age for genome-wide functional analysis
    • Wu, J., Smith, L.T., Plass, C., and Huang, T.H. 2006. ChIP-chip comes of age for genome-wide functional analysis. Cancer Res. 66: 6899-6902.
    • (2006) Cancer Res , vol.66 , pp. 6899-6902
    • Wu, J.1    Smith, L.T.2    Plass, C.3    Huang, T.H.4
  • 40
    • 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
  • 41
    • 10044254753 scopus 로고    scopus 로고
    • E2Fs link the control of G1/S and G2/M transcription
    • Zhu, W., Giangrande, P.H., and Nevins, J.R. 2004. E2Fs link the control of G1/S and G2/M transcription. EMBO J. 23: 4615-4626.
    • (2004) EMBO J , vol.23 , pp. 4615-4626
    • Zhu, W.1    Giangrande, P.H.2    Nevins, J.R.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.