메뉴 건너뛰기




Volumn 28, Issue 8, 2011, Pages 2173-2183

Evolution of promoter affinity for transcription factors in the human lineage

Author keywords

adaptive evolution; regulatory evolution; transcriptional regulation

Indexed keywords

HEPATOCYTE NUCLEAR FACTOR 1ALPHA; HEPATOCYTE NUCLEAR FACTOR 3BETA; HEPATOCYTE NUCLEAR FACTOR 4ALPHA; MYC PROTEIN; OCTAMER TRANSCRIPTION FACTOR 4; PROTEIN P53; STAT1 PROTEIN; TRANSCRIPTION FACTOR GATA 1; TRANSCRIPTION FACTOR SOX2;

EID: 79961071787     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msr027     Document Type: Article
Times cited : (23)

References (33)
  • 2
    • 77955877436 scopus 로고    scopus 로고
    • An alignment-free method to identify candidate orthologous enhancers in multiple drosophila genomes
    • Arunachalam M, Jayasurya K, Tomancak P, Ohler U. 2010. An alignment-free method to identify candidate orthologous enhancers in multiple drosophila genomes. Bioinformatics 26(17):2109-2115.
    • (2010) Bioinformatics , vol.26 , Issue.17 , pp. 2109-2115
    • Arunachalam, M.1    Jayasurya, K.2    Tomancak, P.3    Ohler, U.4
  • 3
    • 55549117831 scopus 로고    scopus 로고
    • Evolution of the mammalian transcription factor binding repertoire via transposable elements
    • 11 co-authors
    • Bourque G, Leong B, Vega VB, et al. (11 co-authors). 2008. Evolution of the mammalian transcription factor binding repertoire via transposable elements. Genome Res. 18(11):1752-1762.
    • (2008) Genome Res. , vol.18 , Issue.11 , pp. 1752-1762
    • Bourque, G.1    Leong, B.2    Vega, V.B.3
  • 6
    • 22744439568 scopus 로고    scopus 로고
    • Evolution at two levels: On genes and form
    • Carroll SB. 2005. Evolution at two levels: on genes and form. PLoS Biol. 3(7):e245.
    • (2005) PLoS Biol. , vol.3 , Issue.7
    • Carroll, S.B.1
  • 7
    • 65349162170 scopus 로고    scopus 로고
    • Conservation of core gene expression in vertebrate tissues
    • 12 co-authors
    • Chan E, Quon G, Chua G, et al. (12 co-authors). 2009. Conservation of core gene expression in vertebrate tissues. J Biol. 8(3):33.
    • (2009) J Biol. , vol.8 , Issue.3 , pp. 33
    • Chan, E.1    Quon, G.2    Chua, G.3
  • 9
    • 33745593963 scopus 로고    scopus 로고
    • Evolution of candidate transcriptional regulatory motifs since the human-chimpanzee divergence
    • Donaldson IJ, Göttgens B. 2006. Evolution of candidate transcriptional regulatory motifs since the human-chimpanzee divergence. Genome Biol. 7(6):R52.
    • (2006) Genome Biol. , vol.7 , Issue.6
    • Donaldson, I.J.1    Göttgens, B.2
  • 10
    • 22344437987 scopus 로고    scopus 로고
    • Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach
    • Elemento O, Tavazoie S. 2005. Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach. Genome Biol. 6(2):R18.
    • (2005) Genome Biol. , vol.6 , Issue.2
    • Elemento, O.1    Tavazoie, S.2
  • 11
  • 12
    • 33748191291 scopus 로고    scopus 로고
    • Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE
    • DOI 10.1093/bioinformatics/btl223
    • Foat BC, Morozov AV, Bussemaker HJ. 2006. Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE. Bioinformatics 22(14):e141-e149. (Pubitemid 44307813)
    • (2006) Bioinformatics , vol.22 , Issue.14
    • Foat, B.C.1    Morozov, A.V.2    Bussemaker, H.J.3
  • 13
    • 68049102316 scopus 로고    scopus 로고
    • Exaptation of an ancient Alu short interspersed element provides a highly conserved vitamin dmediated innate immune response in humans and primates
    • Gombart AF, Saito T, Koeffler HP. 2009. Exaptation of an ancient Alu short interspersed element provides a highly conserved vitamin dmediated innate immune response in humans and primates. BMC Genomics 10:321.
    • (2009) BMC Genomics , vol.10 , pp. 321
    • Gombart, A.F.1    Saito, T.2    Koeffler, H.P.3
  • 14
    • 71749120382 scopus 로고    scopus 로고
    • Finding distal regulatory elements in the human genome
    • Heintzman ND, Ren B. 2009. Finding distal regulatory elements in the human genome. Curr Opin Genet Dev. 19(6):541-549.
    • (2009) Curr Opin Genet Dev. , vol.19 , Issue.6 , pp. 541-549
    • Heintzman, N.D.1    Ren, B.2
  • 15
    • 34547844142 scopus 로고    scopus 로고
    • A statistical method for alignment-free comparison of regulatory sequences
    • DOI 10.1093/bioinformatics/btm211
    • Kantorovitz MR, Robinson GE, Sinha S. 2007. A statistical method for alignment-free comparison of regulatory sequences. Bioinformatics 23(13):i249-i255. (Pubitemid 47244407)
    • (2007) Bioinformatics , vol.23 , Issue.13
    • Kantorovitz, M.R.1    Robinson, G.E.2    Sinha, S.3
  • 16
    • 22144447840 scopus 로고    scopus 로고
    • Evolution: Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees
    • DOI 10.1126/science.1108296
    • Khaitovich P, Hellmann I, Enard W, Nowick K, Leinweber M, Franz H, Weiss G, Lachmann M, Pääbo S. 2005. Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees. Science 309(5742):1850-1854. (Pubitemid 41325094)
    • (2005) Science , vol.309 , Issue.5742 , pp. 1850-1854
    • Khaitovich, P.1    Hellmann, I.2    Enard, W.3    Nowick, K.4    Leinweber, M.5    Franz, H.6    Weiss, G.7    Lachmann, M.8    Paabo, S.9
  • 17
    • 0016669094 scopus 로고
    • Evolution at two levels in humans and chimpanzees
    • King MC, Wilson AC. 1975. Evolution at two levels in humans and chimpanzees. Science 188(4184):107-116.
    • (1975) Science , vol.188 , Issue.4184 , pp. 107-116
    • King, M.C.1    Wilson, A.C.2
  • 18
  • 21
    • 75549089967 scopus 로고    scopus 로고
    • The UCSC genome browser database: Update 2010
    • 23 co-authors, Database issue
    • Rhead B, Karolchik D, Kuhn RM, et al. (23 co-authors). 2010. The UCSC genome browser database: update 2010. Nucleic Acids Res. 38(Database issue):D613-D619.
    • (2010) Nucleic Acids Res. , vol.38
    • Rhead, B.1    Karolchik, D.2    Kuhn, R.M.3
  • 24
    • 77955342465 scopus 로고    scopus 로고
    • Mer41 repeat sequences contain inducible stat1 binding sites
    • Schmid CD, Bucher P. 2010. Mer41 repeat sequences contain inducible stat1 binding sites. PLoS One 5(7):e11425.
    • (2010) PLoS One , vol.5 , Issue.7
    • Schmid, C.D.1    Bucher, P.2
  • 25
    • 38749127589 scopus 로고    scopus 로고
    • Predicting expression patterns from regulatory sequence in Drosophila segmentation
    • DOI 10.1038/nature06496, PII NATURE06496
    • Segal E, Raveh-Sadka T, Schroeder M, Unnerstall U, Gaul U. 2008. Predicting expression patterns from regulatory sequence in Drosophila segmentation. Nature 451(7178):535-540. (Pubitemid 351186263)
    • (2008) Nature , vol.451 , Issue.7178 , pp. 535-540
    • Segal, E.1    Raveh-Sadka, T.2    Schroeder, M.3    Unnerstall, U.4    Gaul, U.5
  • 27
    • 70149100044 scopus 로고    scopus 로고
    • Evolutionary processes acting on candidate cis-regulatory regions in humans inferred from patterns of polymorphism and divergence
    • 11 co-authors
    • Torgerson DG, Boyko AR, Hernandez RD, et al. (11 co-authors). 2009. Evolutionary processes acting on candidate cis-regulatory regions in humans inferred from patterns of polymorphism and divergence. PLoS Genet. 5(8):e1000592.
    • (2009) PLoS Genet. , vol.5 , Issue.8
    • Torgerson, D.G.1    Boyko, A.R.2    Hernandez, R.D.3
  • 28
    • 1342309208 scopus 로고    scopus 로고
    • Metrics for comparing regulatory sequences on the basis of pattern counts
    • van Helden J. 2004. Metrics for comparing regulatory sequences on the basis of pattern counts. Bioinformatics 20(3):399-406.
    • (2004) Bioinformatics , vol.20 , Issue.3 , pp. 399-406
    • Van Helden, J.1
  • 30
    • 46249089455 scopus 로고    scopus 로고
    • Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences
    • DOI 10.1093/bioinformatics/btn154
    • Ward LD, Bussemaker HJ. 2008. Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences. Bioinformatics 24(13):i165-i171. (Pubitemid 351911670)
    • (2008) Bioinformatics , vol.24 , Issue.13
    • Ward, L.D.1    Bussemaker, H.J.2
  • 31
    • 33847057226 scopus 로고    scopus 로고
    • The evolutionary significance of cis-regulatory mutations
    • Wray GA. 2007. The evolutionary significance of cis-regulatory mutations. Nat Rev Genet. 8(3):206-216.
    • (2007) Nat Rev Genet. , vol.8 , Issue.3 , pp. 206-216
    • Wray, G.A.1
  • 32
    • 67949111078 scopus 로고    scopus 로고
    • Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships
    • Yokoyama KD, Ohler U, Wray GA. 2009. Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships. Nucleic Acids Res. 37(13):e92.
    • (2009) Nucleic Acids Res. , vol.37 , Issue.13
    • Yokoyama, K.D.1    Ohler, U.2    Wray, G.A.3
  • 33
    • 77149125896 scopus 로고    scopus 로고
    • Systematic analysis, comparison, and integration of disease based human genetic association data and mouse genetic phenotypic information
    • Zhang Y, De S, Garner JR, Smith K, Wang SA, Becker KG. 2010. Systematic analysis, comparison, and integration of disease based human genetic association data and mouse genetic phenotypic information. BMC Med Genomics 3:1.
    • (2010) BMC Med Genomics , vol.3 , pp. 1
    • Zhang, Y.1    De, S.2    Garner, J.R.3    Smith, K.4    Wang, S.A.5    Becker, K.G.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.