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Volumn 917, Issue , 2012, Pages 245-263

Comparative genomics-based identification and analysis of cis-regulatory elements

Author keywords

Cis regulatory elements; Comparative genomics; Enhancer; Multiple alignment; Phylogenetic footprinting; Transcription factor binding motif; Xenopus transgenesis

Indexed keywords


EID: 84868562425     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-992-1_15     Document Type: Article
Times cited : (8)

References (32)
  • 1
    • 1842584947 scopus 로고    scopus 로고
    • Applied bioinformatics for the identification of regulatory elements
    • DOI 10.1038/nrg1315
    • Wasserman WW, Sandelin A (2004) Applied bioinformatics for the identi fication of regulatory elements. Nat Rev Genet 5:276-287 (Pubitemid 38435623)
    • (2004) Nature Reviews Genetics , vol.5 , Issue.4 , pp. 276-287
    • Wasserman, W.W.1    Sandelin, A.2
  • 3
    • 20044366725 scopus 로고    scopus 로고
    • Highly conserved noncoding sequences are associated with vertebrate development
    • Woolfe A et al (2005) Highly conserved noncoding sequences are associated with vertebrate development. PLoS Biol 3:e7
    • (2005) PLoS Biol , vol.3
    • Woolfe, A.1
  • 6
    • 61349104285 scopus 로고    scopus 로고
    • Highly conserved noncoding elements on either side of SOX9 associated with Pierre Robin sequence
    • Benko S et al (2009) Highly conserved noncoding elements on either side of SOX9 associated with Pierre Robin sequence. Nat Genet 41:359-364
    • (2009) Nat Genet , vol.41 , pp. 359-364
    • Benko, S.1
  • 7
    • 33645833857 scopus 로고    scopus 로고
    • Conservation of RET regulatory function from human to zebra fish without sequence similarity
    • Fisher S et al (2006) Conservation of RET regulatory function from human to zebra fish without sequence similarity. Science 312:276-279
    • (2006) Science , vol.312 , pp. 276-279
    • Fisher, S.1
  • 8
    • 60149091656 scopus 로고    scopus 로고
    • ChIP-seq accurately predicts tissue-specific activity of enhancers
    • Visel A et al (2009) ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457:854-858
    • (2009) Nature , vol.457 , pp. 854-858
    • Visel, A.1
  • 9
    • 77951823093 scopus 로고    scopus 로고
    • The genome of the Western clawed frog Xenopus tropicalis
    • Hellsten U et al (2010) The genome of the Western clawed frog Xenopus tropicalis . Science 328:633-636
    • (2010) Science , vol.328 , pp. 633-636
    • Hellsten, U.1
  • 11
    • 36248946042 scopus 로고    scopus 로고
    • Evolutionary developmental biology and genomics
    • DOI 10.1038/nrg2226, PII NRG2226
    • Canestro C, Yokoi H, Postlethwait JH (2007) Evolutionary developmental biology and genomics. Nat Rev Genet 8:932-942 (Pubitemid 350129173)
    • (2007) Nature Reviews Genetics , vol.8 , Issue.12 , pp. 932-942
    • Caestro, C.1    Yokoi, H.2    Postlethwait, J.H.3
  • 12
    • 38949142986 scopus 로고    scopus 로고
    • Convergence of a head-field selector Otx2 and Notch signaling: A mechanism for lens specification
    • DOI 10.1242/dev.009548
    • Ogino H, Fisher M, Grainger RM (2008) Convergence of a head- field selector Otx2 and Notch signaling: A mechanism for lens specification. Development 135:249-258 (Pubitemid 351228417)
    • (2008) Development , vol.135 , Issue.2 , pp. 249-258
    • Ogino, H.1    Fisher, M.2    Grainger, R.M.3
  • 13
    • 3242878193 scopus 로고    scopus 로고
    • ECR Browser: A tool for visualizing and accessing data from comparisons of multiple vertebrate genomes
    • DOI 10.1093/nar/gkh355
    • Ovcharenko I et al (2004) ECR Browser: A tool for visualizing and accessing data from comparisons of multiple vertebrate genomes. Nucleic Acids Res 32:W280-W286 (Pubitemid 38997344)
    • (2004) Nucleic Acids Research , vol.32 , Issue.WEB SERVER ISS.
    • Ovcharenko, I.1    Nobrega, M.A.2    Loots, G.G.3    Stubbs, L.4
  • 16
    • 26444591973 scopus 로고    scopus 로고
    • Genomic regulatory networks and animal development
    • DOI 10.1016/j.devcel.2005.09.005, PII S1534580705003400
    • Stathopoulos A, Levine M (2005) Genomic regulatory networks and animal development. Dev Cell 9:449-462 (Pubitemid 41430729)
    • (2005) Developmental Cell , vol.9 , Issue.4 , pp. 449-462
    • Stathopoulos, A.1    Levine, M.2
  • 17
    • 3242888285 scopus 로고    scopus 로고
    • RVISTA 2.0: Evolutionary analysis of transcription factor binding sites
    • DOI 10.1093/nar/gkh383
    • Loots GG, Ovcharenko I (2004) rVISTA 2.0: evolutionary analysis of transcription factor binding sites. Nucleic Acids Res 32: W217-W221 (Pubitemid 38997333)
    • (2004) Nucleic Acids Research , vol.32 , Issue.WEB SERVER ISS.
    • Loots, G.G.1    Ovcharenko, I.2
  • 18
    • 3242891274 scopus 로고    scopus 로고
    • ConSite: Web-based prediction of regulatory elements using cross-species comparison
    • DOI 10.1093/nar/gkh372
    • Sandelin A, Wasserman WW, Lenhard B (2004) ConSite: web-based prediction of regulatory elements using cross-species comparison. Nucleic Acids Res 32:W249-W252 (Pubitemid 38997338)
    • (2004) Nucleic Acids Research , vol.32 , Issue.WEB SERVER ISS.
    • Sandelin, A.1    Wasserman, W.W.2    Lenhard, B.3
  • 19
    • 75549083247 scopus 로고    scopus 로고
    • JASPAR 2010: The greatly expanded open-access database of transcription factor binding pro files
    • Portales-Casamar E et al (2010) JASPAR 2010: the greatly expanded open-access database of transcription factor binding pro files. Nucleic Acids Res 38:D105-D110
    • (2010) Nucleic Acids Res , vol.38
    • Portales-Casamar, E.1
  • 21
    • 0021100423 scopus 로고
    • The nucleotide sequence of the chick cytoplasmic b -actin gene
    • Kost TA, Theodorakis N, Hughes SH (1983) The nucleotide sequence of the chick cytoplasmic b -actin gene. Nucleic Acids Res 11:8287-8301
    • (1983) Nucleic Acids Res , vol.11 , pp. 8287-8301
    • Kost, T.A.1    Theodorakis, N.2    Hughes, S.H.3
  • 22
    • 60549097668 scopus 로고    scopus 로고
    • Systematic human/zebra fish comparative identi fication of cis-regulatory activity around vertebrate developmental transcription factor genes
    • Navratilova P et al (2009) Systematic human/zebra fish comparative identi fication of cis-regulatory activity around vertebrate developmental transcription factor genes. Dev Biol 327:526-540
    • (2009) Dev Biol , vol.327 , pp. 526-540
    • Navratilova, P.1
  • 24
    • 0032942213 scopus 로고    scopus 로고
    • Regulation of Pax6 expression is conserved between mice and fl ies
    • Xu PX et al (1999) Regulation of Pax6 expression is conserved between mice and fl ies. Development 126:383-395
    • (1999) Development , vol.126 , pp. 383-395
    • Xu, P.X.1
  • 25
    • 65449188232 scopus 로고    scopus 로고
    • Jalview version 2 - A multiple sequence alignment editor and analysis workbench
    • Waterhouse AM et al (2009) Jalview version 2 - a multiple sequence alignment editor and analysis workbench. Bioinformatics 25: 1189-1191
    • (2009) Bioinformatics , vol.25 , pp. 1189-1191
    • Waterhouse, A.M.1
  • 26
    • 79951516056 scopus 로고    scopus 로고
    • A unique chromatin signature uncovers early developmental enhancers in humans
    • Rada-Iglesias A et al (2011) A unique chromatin signature uncovers early developmental enhancers in humans. Nature 470:279-283
    • (2011) Nature , vol.470 , pp. 279-283
    • Rada-Iglesias, A.1
  • 27
    • 45449111373 scopus 로고    scopus 로고
    • Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites
    • DOI 10.1016/j.cell.2008.05.023, PII S009286740800682X
    • Noyes MB et al (2008) Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites. Cell 133:1277-1289 (Pubitemid 351852912)
    • (2008) Cell , vol.133 , Issue.7 , pp. 1277-1289
    • Noyes, M.B.1    Christensen, R.G.2    Wakabayashi, A.3    Stormo, G.D.4    Brodsky, M.H.5    Wolfe, S.A.6
  • 28
    • 0028352067 scopus 로고
    • Illegitimate recombination in Xenopus: Characterization of end-joined junctions
    • Lehman CW, Trautman JK, Carroll D (1994) Illegitimate recombination in Xenopus : characterization of end-joined junctions. Nucleic Acids Res 22:434-442 (Pubitemid 24160866)
    • (1994) Nucleic Acids Research , vol.22 , Issue.3 , pp. 434-442
    • Lehman, C.W.1    Trautman, J.K.2    Carroll, D.3
  • 30
    • 65349094090 scopus 로고    scopus 로고
    • Resources and transgenesis techniques for functional genomics in Xenopus
    • Ogino H, Ochi H (2009) Resources and transgenesis techniques for functional genomics in Xenopus . Dev Growth Differ 51:387-401
    • (2009) Dev Growth Differ , vol.51 , pp. 387-401
    • Ogino, H.1    Ochi, H.2
  • 31
    • 34248641108 scopus 로고    scopus 로고
    • High-throughput transgenesis in Xenopus using I-SceI meganuclease
    • DOI 10.1038/nprot.2006.208, PII NPROT.2006.208
    • Ogino H, McConnell WB, Grainger RM (2006) High-throughput transgenesis in Xenopus using I-SceI meganuclease. Nat Protoc 1:1703-1710 (Pubitemid 46773291)
    • (2006) Nature Protocols , vol.1 , Issue.4 , pp. 1703-1710
    • Ogino, H.1    McConnell, W.B.2    Grainger, R.M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.