메뉴 건너뛰기




Volumn 8, Issue 1, 2007, Pages

Detection of weakly conserved ancestral mammalian regulatory sequences by primate comparisons

Author keywords

[No Author keywords available]

Indexed keywords

CHOLESTEROL; DNA; SPACER DNA; STEROL REGULATORY ELEMENT BINDING PROTEIN 1;

EID: 34147170895     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2007-8-1-r1     Document Type: Article
Times cited : (24)

References (28)
  • 3
    • 33745628791 scopus 로고    scopus 로고
    • Close sequence comparisons are sufficient to identify human cis-regulatory elements
    • 16769978 10.1101/gr.4717506 1484452
    • Prabhakar S Poulin F Shoukry M Afzal V Rubin EM Couronne O Pennacchio LA Close sequence comparisons are sufficient to identify human cis-regulatory elements. Genome Res 2006 16 855-863 16769978 10.1101/ gr.4717506 1484452
    • (2006) Genome Res , vol.16 , pp. 855-863
    • Prabhakar, S.1    Poulin, F.2    Shoukry, M.3    Afzal, V.4    Rubin, E.M.5    Couronne, O.6    Pennacchio, L.A.7
  • 4
    • 33645833857 scopus 로고    scopus 로고
    • Conservation of RET regulatory function from human to zebrafish without sequence similarity
    • 16556802 10.1126/science.1124070
    • Fisher S Grice EA Vinton RM Bessling SL McCallion AS Conservation of RET regulatory function from human to zebrafish without sequence similarity. Science 2006 312 276-279 16556802 10.1126/science.1124070
    • (2006) Science , vol.312 , pp. 276-279
    • Fisher, S.1    Grice, E.A.2    Vinton, R.M.3    Bessling, S.L.4    McCallion, A.S.5
  • 5
    • 3042740671 scopus 로고    scopus 로고
    • Comparative genomics at the vertebrate extremes
    • 15153998 10.1038/nrg1350
    • Boffelli D Nobrega MA Rubin EM Comparative genomics at the vertebrate extremes. Nat Rev Genet 2004 5 456-465 15153998 10.1038/nrg1350
    • (2004) Nat Rev Genet , vol.5 , pp. 456-465
    • Boffelli, D.1    Nobrega, M.A.2    Rubin, E.M.3
  • 6
    • 0242418246 scopus 로고    scopus 로고
    • Phylogenetic shadowing of primate sequences to find functional regions of the human genome
    • 12610304 10.1126/science.1081331
    • Boffelli D McAuliffe J Ovcharenko D Lewis KD Ovcharenko I Pachter L Rubin EM Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science 2003 299 1391-1394 12610304 10.1126/ science.1081331
    • (2003) Science , vol.299 , pp. 1391-1394
    • Boffelli, D.1    McAuliffe, J.2    Ovcharenko, D.3    Lewis, K.D.4    Ovcharenko, I.5    Pachter, L.6    Rubin, E.M.7
  • 7
    • 3543149022 scopus 로고    scopus 로고
    • Identifying candidate causal variants responsible for altered activity of the ABCB1 multidrug resistance gene
    • 15197162 10.1101/gr.1965304 442149
    • Soranzo N Cavalleri GL Weale ME Wood NW Depondt C Marguerie R Sisodiya SM Goldstein DB Identifying candidate causal variants responsible for altered activity of the ABCB1 multidrug resistance gene. Genome Res 2004 14 1333-1344 15197162 10.1101/gr.1965304 442149
    • (2004) Genome Res , vol.14 , pp. 1333-1344
    • Soranzo, N.1    Cavalleri, G.L.2    Weale, M.E.3    Wood, N.W.4    Depondt, C.5    Marguerie, R.6    Sisodiya, S.M.7    Goldstein, D.B.8
  • 8
    • 0036668184 scopus 로고    scopus 로고
    • Bile acid regulation of gene expression: Roles of nuclear hormone receptors
    • 12202460 10.1210/er.2000-0035
    • Chiang JY Bile acid regulation of gene expression: Roles of nuclear hormone receptors. Endocr Rev 2002 23 443-463 12202460 10.1210/ er.2000-0035
    • (2002) Endocr Rev , vol.23 , pp. 443-463
    • Chiang, J.Y.1
  • 9
    • 27544443178 scopus 로고    scopus 로고
    • Mapping cis-regulatory domains in the human genome using multi-species conservation of synteny
    • 16155111 10.1093/hmg/ddi338
    • Ahituv N Prabhakar S Poulin F Rubin EM Couronne O Mapping cis-regulatory domains in the human genome using multi-species conservation of synteny. Hum Mol Genet 2005 14 3057-3063 16155111 10.1093/hmg/ddi338
    • (2005) Hum Mol Genet , vol.14 , pp. 3057-3063
    • Ahituv, N.1    Prabhakar, S.2    Poulin, F.3    Rubin, E.M.4    Couronne, O.5
  • 10
    • 22244458301 scopus 로고    scopus 로고
    • Annotation of cis-regulatory elements by identification, subclassification, and functional assessment of multispecies conserved sequences
    • 15998734 10.1073/pnas.0503401102 1174996
    • Hughes JR Cheng JF Ventress N Prabhakar S Clark K Anguita E De Gobbi M de Jong P Rubin E Higgs DR Annotation of cis-regulatory elements by identification, subclassification, and functional assessment of multispecies conserved sequences. Proc Natl Acad Sci USA 2005 102 9830-9835 15998734 10.1073/pnas.0503401102 1174996
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 9830-9835
    • Hughes, J.R.1    Cheng, J.F.2    Ventress, N.3    Prabhakar, S.4    Clark, K.5    Anguita, E.6    De Gobbi, M.7    de Jong, P.8    Rubin, E.9    Higgs, D.R.10
  • 11
    • 14644390333 scopus 로고    scopus 로고
    • A model of the statistical power of comparative genome sequence analysis
    • 15660152 10.1371/journal.pbio.0030010 539325
    • Eddy SR A model of the statistical power of comparative genome sequence analysis. PLoS Biology 2005 3 e10 15660152 10.1371/journal.pbio.0030010 539325
    • (2005) PLoS Biology , vol.3
    • Eddy, S.R.1
  • 13
    • 46249105110 scopus 로고    scopus 로고
    • UCSC Genome Browser http://genome.ucsc.edu
  • 14
    • 0035830840 scopus 로고    scopus 로고
    • Unsaturated fatty acids down-regulate SREBP isoforms 1a and 1c by two mechanisms in HEK-293 Cells
    • 11085986 10.1074/jbc.M007273200
    • Hannah VC Ou J Luong A Goldstein JL Brown MS Unsaturated fatty acids down-regulate SREBP isoforms 1a and 1c by two mechanisms in HEK-293 Cells. J Biol Chem 2001 276 4365-4372 11085986 10.1074/jbc.M007273200
    • (2001) J Biol Chem , vol.276 , pp. 4365-4372
    • Hannah, V.C.1    Ou, J.2    Luong, A.3    Goldstein, J.L.4    Brown, M.S.5
  • 15
    • 0037398368 scopus 로고    scopus 로고
    • LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA
    • 12654723 10.1101/gr.926603 430158
    • Brudno M Do CB Cooper GM Kim MF Davydov E Green ED Sidow A Batzoglou S LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA. Genome Res 2003 13 721-731 12654723 10.1101/ gr.926603 430158
    • (2003) Genome Res , vol.13 , pp. 721-731
    • Brudno, M.1    Do, C.B.2    Cooper, G.M.3    Kim, M.F.4    Davydov, E.5    Green, E.D.6    Sidow, A.7    Batzoglou, S.8
  • 16
    • 3042558659 scopus 로고    scopus 로고
    • eShadow: A tool for comparing closely related sequences
    • 15173121 10.1101/gr.1773104 419798
    • Ovcharenko I Boffelli D Loots GG eShadow: A tool for comparing closely related sequences. Genome Res 2004 14 1191-1198 15173121 10.1101/ gr.1773104 419798
    • (2004) Genome Res , vol.14 , pp. 1191-1198
    • Ovcharenko, I.1    Boffelli, D.2    Loots, G.G.3
  • 18
    • 17744380974 scopus 로고    scopus 로고
    • Making very similar embryos with divergent genomes: Conservation of regulatory mechanisms of Otx between the ascidians Halocynthia roretzi and Ciona intestinalis
    • 15743880 10.1242/dev.01707
    • Oda-Ishii I Bertrand V Matsuo I Lemaire P Saiga H Making very similar embryos with divergent genomes: Conservation of regulatory mechanisms of Otx between the ascidians Halocynthia roretzi and Ciona intestinalis. Development 2005 132 1663-1674 15743880 10.1242/dev.01707
    • (2005) Development , vol.132 , pp. 1663-1674
    • Oda-Ishii, I.1    Bertrand, V.2    Matsuo, I.3    Lemaire, P.4    Saiga, H.5
  • 19
    • 0034598832 scopus 로고    scopus 로고
    • Evidence for stabilizing selection in a eukaryotic enhancer element
    • 10676967 10.1038/35000615
    • Ludwig MZ Bergman C Patel NH Kreitman M Evidence for stabilizing selection in a eukaryotic enhancer element. Nature 2000 403 564-567 10676967 10.1038/35000615
    • (2000) Nature , vol.403 , pp. 564-567
    • Ludwig, M.Z.1    Bergman, C.2    Patel, N.H.3    Kreitman, M.4
  • 20
    • 46249113124 scopus 로고    scopus 로고
    • BACPAC Resources http://bacpac.chori.org
  • 22
    • 0030663731 scopus 로고    scopus 로고
    • Two hepatic enhancers, HCR.1 and HCR.2, coordinate the liver expression of the entire human apolipoprotein E/C-I/C-IV/C-II gene cluster
    • 9360987 10.1074/jbc.272.46.29113
    • Allan CM Taylor S Taylor JM Two hepatic enhancers, HCR.1 and HCR.2, coordinate the liver expression of the entire human apolipoprotein E/C-I/ C-IV/C-II gene cluster. J Biol Chem 1997 272 29113 29119-9360987 10.1074/ jbc.272.46.29113
    • (1997) J Biol Chem , vol.272 , pp. 29113-29119
    • Allan, C.M.1    Taylor, S.2    Taylor, J.M.3
  • 23
    • 0037199994 scopus 로고    scopus 로고
    • Regulated expression of the apolipoprotein E/C-I/C-IV/C-II gene cluster in murine and human macrophages. A critical role for nuclear liver X receptors alpha and beta
    • 12032151 10.1074/jbc.M202993200
    • Mak PA Laffitte BA Desrumaux C Joseph SB Curtiss LK Mangelsdorf DJ Tontonoz P Edwards PA Regulated expression of the apolipoprotein E/C-I/ C-IV/C-II gene cluster in murine and human macrophages. A critical role for nuclear liver X receptors alpha and beta. J Biol Chem 2002 277 31900-31908-12032151 10.1074/jbc.M202993200
    • (2002) J Biol Chem , vol.277 , pp. 31900-31908
    • Mak, P.A.1    Laffitte, B.A.2    Desrumaux, C.3    Joseph, S.B.4    Curtiss, L.K.5    Mangelsdorf, D.J.6    Tontonoz, P.7    Edwards, P.A.8
  • 24
    • 0036105591 scopus 로고    scopus 로고
    • rVista for comparative sequence-based discovery of functional transcription factor binding sites
    • 11997350 10.1101/gr.225502. Article published online before print in April 2002 186580
    • Loots GG Ovcharenko I Pachter L Dubchak I Rubin EM rVista for comparative sequence-based discovery of functional transcription factor binding sites. Genome Res 2002 12 832-839 11997350 10.1101/gr.225502. Article published online before print in April 2002 186580
    • (2002) Genome Res , vol.12 , pp. 832-839
    • Loots, G.G.1    Ovcharenko, I.2    Pachter, L.3    Dubchak, I.4    Rubin, E.M.5
  • 25
    • 46249115283 scopus 로고    scopus 로고
    • VISTA Browser http://pipeline.lbl.gov/
  • 26
    • 0027957393 scopus 로고
    • fastDNAmL: A tool for construction of phylogenetic trees of DNA sequences using maximum likelihood
    • 8193955
    • Olsen GJ Matsuda H Hagstrom R Overbeek R fastDNAmL: A tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Comput Appl Biosci 1994 10 41-48 8193955
    • (1994) Comput Appl Biosci , vol.10 , pp. 41-48
    • Olsen, G.J.1    Matsuda, H.2    Hagstrom, R.3    Overbeek, R.4
  • 27
    • 0037348748 scopus 로고    scopus 로고
    • Progress and prospects: Naked DNA gene transfer and therapy
    • 12621449 10.1038/sj.gt.3301983
    • Herweijer H Wolff JA Progress and prospects: Naked DNA gene transfer and therapy. Gene Ther 2003 10 453-458 12621449 10.1038/sj.gt.3301983
    • (2003) Gene Ther , vol.10 , pp. 453-458
    • Herweijer, H.1    Wolff, J.A.2
  • 28
    • 0037205439 scopus 로고    scopus 로고
    • Activation of vascular endothelial growth factor A transcription in tumorigenic glioblastoma cell lines by an enhancer with cell type-specific DNase I accessibility
    • 11912213 10.1074/jbc.M201766200
    • Liang Y Li XY Rebar EJ Li P Zhou Y Chen B Wolffe AP Case CC Activation of vascular endothelial growth factor A transcription in tumorigenic glioblastoma cell lines by an enhancer with cell type-specific DNase I accessibility. J Biol Chem 2002 277 20087-20094 11912213 10.1074/ jbc.M201766200
    • (2002) J Biol Chem , vol.277 , pp. 20087-20094
    • Liang, Y.1    Li, X.Y.2    Rebar, E.J.3    Li, P.4    Zhou, Y.5    Chen, B.6    Wolffe, A.P.7    Case, C.C.8


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.