메뉴 건너뛰기




Volumn 11, Issue 1, 2010, Pages

Touring Ensembl: A practical guide to genome browsing

Author keywords

[No Author keywords available]

Indexed keywords

INTERLEUKIN 2; MYOSIN VI;

EID: 77951962908     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-295     Document Type: Article
Times cited : (25)

References (63)
  • 1
    • 58149185138 scopus 로고    scopus 로고
    • Nucleic Acids Research annual Database Issue and the NAR online Molecular Biology Database Collection in 2009
    • Database
    • Galperin MY, Cochrane GR. Nucleic Acids Research annual Database Issue and the NAR online Molecular Biology Database Collection in 2009. Nucleic Acids Res 2009, (37 Database):D1-4.
    • (2009) Nucleic Acids Res , Issue.37
    • Galperin, M.Y.1    Cochrane, G.R.2
  • 3
    • 33846057724 scopus 로고    scopus 로고
    • NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
    • 10.1093/nar/gkl842, 1716718, 17130148, Database
    • Pruitt KD, Tatusova T, Maglott DR. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 2007, (35 Database):D61-5. 10.1093/nar/gkl842, 1716718, 17130148.
    • (2007) Nucleic Acids Res , Issue.35
    • Pruitt, K.D.1    Tatusova, T.2    Maglott, D.R.3
  • 4
    • 0033539168 scopus 로고    scopus 로고
    • CpG islands as genomic footprints of promoters that are associated with replication origins
    • Antequera F, Bird A. CpG islands as genomic footprints of promoters that are associated with replication origins. Curr Biol 1999, 9:R661-7.
    • (1999) Curr Biol , vol.9
    • Antequera, F.1    Bird, A.2
  • 6
    • 67849095416 scopus 로고    scopus 로고
    • BioMart Central Portal--unified access to biological data
    • 10.1093/nar/gkp265, 2703988, 19420058, Web Server
    • Haider S, Ballester B, Smedley D, Zhang J, Rice P, Kasprzyk A. BioMart Central Portal--unified access to biological data. Nucleic Acids Res 2009, (37 Web Server):W23-7. 10.1093/nar/gkp265, 2703988, 19420058.
    • (2009) Nucleic Acids Res , Issue.37
    • Haider, S.1    Ballester, B.2    Smedley, D.3    Zhang, J.4    Rice, P.5    Kasprzyk, A.6
  • 8
    • 2942547885 scopus 로고    scopus 로고
    • The distributed annotation system
    • 10.1186/1471-2105-2-7, 58584, 11667947
    • Dowell RD, Jokerst RM, Day A, Eddy SR, Stein L. The distributed annotation system. BMC Bioinformatics 2001, 2(1):7. 10.1186/1471-2105-2-7, 58584, 11667947.
    • (2001) BMC Bioinformatics , vol.2 , Issue.1 , pp. 7
    • Dowell, R.D.1    Jokerst, R.M.2    Day, A.3    Eddy, S.R.4    Stein, L.5
  • 9
    • 77954316273 scopus 로고    scopus 로고
    • Ensembl Tutorials and Worked Examples
    • Ensembl Tutorials and Worked Examples. , http://www.ensembl.org/info/website/tutorials/index.html
  • 10
    • 40849090414 scopus 로고    scopus 로고
    • Genome browsing with Ensembl: a practical overview
    • 10.1093/bfgp/elm025, 17967807
    • Spudich G, Fernandez-Suarez XM, Birney E. Genome browsing with Ensembl: a practical overview. Brief Funct Genomic Proteomic 2007, 6(3):202-219. 10.1093/bfgp/elm025, 17967807.
    • (2007) Brief Funct Genomic Proteomic , vol.6 , Issue.3 , pp. 202-219
    • Spudich, G.1    Fernandez-Suarez, X.M.2    Birney, E.3
  • 13
    • 0028325344 scopus 로고
    • Structure and analysis of the 5' flanking region of the human interleukin-2 gene
    • Jankevics E, Makarenkova G, Tsimanis A, Grens E. Structure and analysis of the 5' flanking region of the human interleukin-2 gene. Biochim Biophys Acta 1994, 1217(2):235-238.
    • (1994) Biochim Biophys Acta , vol.1217 , Issue.2 , pp. 235-238
    • Jankevics, E.1    Makarenkova, G.2    Tsimanis, A.3    Grens, E.4
  • 14
    • 0029041568 scopus 로고
    • Transcriptional regulation of the IL-2 gene
    • 10.1016/0952-7915(95)80107-3, 7546397
    • Jain J, Loh C, Rao A. Transcriptional regulation of the IL-2 gene. Curr Opin Immunol 1995, 7(3):333-342. 10.1016/0952-7915(95)80107-3, 7546397.
    • (1995) Curr Opin Immunol , vol.7 , Issue.3 , pp. 333-342
    • Jain, J.1    Loh, C.2    Rao, A.3
  • 17
    • 34250305146 scopus 로고    scopus 로고
    • Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    • 10.1038/nature05874, 2212820, 17571346, ENCODE Project Consortium
    • ENCODE Project Consortium Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007, 447(7146):799-816. 10.1038/nature05874, 2212820, 17571346, ENCODE Project Consortium.
    • (2007) Nature , vol.447 , Issue.7146 , pp. 799-816
  • 18
    • 0036270889 scopus 로고    scopus 로고
    • ChIP-chip: a genomic approach for identifying transcription factor binding sites
    • full_text, 12073330
    • Horak CE, Snyder M. ChIP-chip: a genomic approach for identifying transcription factor binding sites. Methods Enzymol 2002, 350:469-483. full_text, 12073330.
    • (2002) Methods Enzymol , vol.350 , pp. 469-483
    • Horak, C.E.1    Snyder, M.2
  • 20
    • 34249026300 scopus 로고    scopus 로고
    • High-resolution profiling of histone methylations in the human genome
    • 10.1016/j.cell.2007.05.009, 17512414
    • Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K. High-resolution profiling of histone methylations in the human genome. Cell 2007, 129(4):823-837. 10.1016/j.cell.2007.05.009, 17512414.
    • (2007) Cell , vol.129 , Issue.4 , pp. 823-837
    • Barski, A.1    Cuddapah, S.2    Cui, K.3    Roh, T.Y.4    Schones, D.E.5    Wang, Z.6    Wei, G.7    Chepelev, I.8    Zhao, K.9
  • 21
    • 0035451090 scopus 로고    scopus 로고
    • CTCF is a uniquely versatile transcription regulator linked to epigenetics and disease
    • 10.1016/S0168-9525(01)02366-6, 11525835
    • Ohlsson R, Renkawitz R, Lobanenkov V. CTCF is a uniquely versatile transcription regulator linked to epigenetics and disease. Trends Genet 2001, 17(9):520-527. 10.1016/S0168-9525(01)02366-6, 11525835.
    • (2001) Trends Genet , vol.17 , Issue.9 , pp. 520-527
    • Ohlsson, R.1    Renkawitz, R.2    Lobanenkov, V.3
  • 23
    • 33947201809 scopus 로고    scopus 로고
    • Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome
    • 10.1016/j.cell.2006.12.048, 2572726, 17382889
    • Kim TH, Abdullaev ZK, Smith AD, Ching KA, Loukinov DI, Green RD, Zhang MQ, Lobanenkov VV, Ren B. Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell 2007, 128(6):1231-1245. 10.1016/j.cell.2006.12.048, 2572726, 17382889.
    • (2007) Cell , vol.128 , Issue.6 , pp. 1231-1245
    • Kim, T.H.1    Abdullaev, Z.K.2    Smith, A.D.3    Ching, K.A.4    Loukinov, D.I.5    Green, R.D.6    Zhang, M.Q.7    Lobanenkov, V.V.8    Ren, B.9
  • 24
    • 77954316384 scopus 로고    scopus 로고
    • Ensembl.org
    • ensembl.org. , http://www.ensembl.org/biomart/martview
  • 25
    • 77954316305 scopus 로고    scopus 로고
    • Ensembl.org regulatory build
    • ensembl.org regulatory build. , http://www.ensembl.org/info/docs/funcgen/index.html
  • 26
    • 22244452677 scopus 로고    scopus 로고
    • Distribution and intensity of constraint in mammalian genomic sequence
    • 10.1101/gr.3577405, 1172034, 15965027, NISC Comparative Sequencing Program
    • Cooper GM, Stone EA, Asimenos G, , Green ED, Batzoglou S, Sidow A. NISC Comparative Sequencing Program Distribution and intensity of constraint in mammalian genomic sequence. Genome Res 2005, 15(7):901-913. 10.1101/gr.3577405, 1172034, 15965027, NISC Comparative Sequencing Program.
    • (2005) Genome Res , vol.15 , Issue.7 , pp. 901-913
    • Cooper, G.M.1    Stone, E.A.2    Asimenos, G.3    Green, E.D.4    Batzoglou, S.5    Sidow, A.6
  • 29
    • 77954315354 scopus 로고    scopus 로고
    • Enhancer
    • enhancer. , http://enhancer.lbl.gov/
  • 30
    • 13844294267 scopus 로고    scopus 로고
    • A role for myosin VI in postsynaptic structure and glutamate receptor endocytosis
    • 10.1083/jcb.200410091, 2171578, 15657400
    • Osterweil E, Wells DG, Mooseker MS. A role for myosin VI in postsynaptic structure and glutamate receptor endocytosis. J Cell Biol 2005, 168(2):329-338. 10.1083/jcb.200410091, 2171578, 15657400.
    • (2005) J Cell Biol , vol.168 , Issue.2 , pp. 329-338
    • Osterweil, E.1    Wells, D.G.2    Mooseker, M.S.3
  • 31
    • 0033569707 scopus 로고    scopus 로고
    • Role of myosin VI in the differentiation of cochlear hair cells
    • 10.1006/dbio.1999.9424, 10525338
    • Self T, Sobe T, Copeland NG, Jenkins NA, Avraham KB, Steel KP. Role of myosin VI in the differentiation of cochlear hair cells. Dev Biol 1999, 214(2):331-341. 10.1006/dbio.1999.9424, 10525338.
    • (1999) Dev Biol , vol.214 , Issue.2 , pp. 331-341
    • Self, T.1    Sobe, T.2    Copeland, N.G.3    Jenkins, N.A.4    Avraham, K.B.5    Steel, K.P.6
  • 32
    • 77954314966 scopus 로고    scopus 로고
    • Gene MYO6
    • Gene MYO6. , http://Mar2010.archive.ensembl.org/Homo_sapiens/Gene/Compara_Ortholog?g=ENSG00000196586
  • 33
    • 59949096873 scopus 로고    scopus 로고
    • EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
    • 10.1101/gr.073585.107, 2652215, 19029536
    • Vilella AJ, Severin J, Ureta-Vidal A, Heng L, Durbin R, Birney E. EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Res 2009, 19(2):327-335. 10.1101/gr.073585.107, 2652215, 19029536.
    • (2009) Genome Res , vol.19 , Issue.2 , pp. 327-335
    • Vilella, A.J.1    Severin, J.2    Ureta-Vidal, A.3    Heng, L.4    Durbin, R.5    Birney, E.6
  • 34
    • 65449188232 scopus 로고    scopus 로고
    • Jalview Version 2--a multiple sequence alignment editor and analysis workbench
    • 10.1093/bioinformatics/btp033, 2672624, 19151095
    • Waterhouse AM, Procter JB, Martin DM, Clamp M, Barton GJ. Jalview Version 2--a multiple sequence alignment editor and analysis workbench. Bioinformatics 2009, 25(9):1189-1191. 10.1093/bioinformatics/btp033, 2672624, 19151095.
    • (2009) Bioinformatics , vol.25 , Issue.9 , pp. 1189-1191
    • Waterhouse, A.M.1    Procter, J.B.2    Martin, D.M.3    Clamp, M.4    Barton, G.J.5
  • 37
    • 84886763841 scopus 로고    scopus 로고
    • Geneontology
    • geneontology. , http://www.geneontology.org
  • 38
    • 77954310951 scopus 로고    scopus 로고
    • Ensembl 57: Gene Ontology (MYO6)
    • Ensembl 57: Gene Ontology (MYO6). , http://Mar2010.archive.ensembl.org/Homo_sapiens/Transcript/GO?g=ENSG00000196586;t=ENST00000428345
  • 39
    • 77954312654 scopus 로고    scopus 로고
    • Ensembl 57: Gene Ontology (Mouse Myo6)
    • Ensembl 57: Gene Ontology (Mouse Myo6). , http://Mar2010.archive.ensembl.org/Mus_musculus/Transcript/GO?db=core;t=ENSMUST00000113268
  • 40
    • 0026742792 scopus 로고
    • CpG islands as gene markers in the human genome
    • 10.1016/0888-7543(92)90024-M, 1505946
    • Larsen F, Gundersen G, Lopez R, Prydz H. CpG islands as gene markers in the human genome. Genomics 1992, 13(4):1095-1107. 10.1016/0888-7543(92)90024-M, 1505946.
    • (1992) Genomics , vol.13 , Issue.4 , pp. 1095-1107
    • Larsen, F.1    Gundersen, G.2    Lopez, R.3    Prydz, H.4
  • 41
    • 0022540321 scopus 로고
    • CpG-rich islands and the function of DNA methylation
    • 10.1038/321209a0, 2423876
    • Bird A. CpG-rich islands and the function of DNA methylation. Nature 1986, 321:209. 10.1038/321209a0, 2423876.
    • (1986) Nature , vol.321 , pp. 209
    • Bird, A.1
  • 42
    • 0035735265 scopus 로고    scopus 로고
    • Computational identification of promoters and first exons in the human genome
    • 10.1038/ng780, 11726928
    • Davuluri RV, Grosse I, Zhang MQ. Computational identification of promoters and first exons in the human genome. Nat Genet 2001, 29(4):412-417. 10.1038/ng780, 11726928.
    • (2001) Nat Genet , vol.29 , Issue.4 , pp. 412-417
    • Davuluri, R.V.1    Grosse, I.2    Zhang, M.Q.3
  • 43
    • 0036123111 scopus 로고    scopus 로고
    • Computational detection and location of transcription start sites in mammalian genomic DNA
    • 10.1101/gr.216102, 155284, 11875034
    • Down TA, Hubbard TJ. Computational detection and location of transcription start sites in mammalian genomic DNA. Genome Res 2002, 12(3):458-461. 10.1101/gr.216102, 155284, 11875034.
    • (2002) Genome Res , vol.12 , Issue.3 , pp. 458-461
    • Down, T.A.1    Hubbard, T.J.2
  • 44
    • 77954311476 scopus 로고    scopus 로고
    • The DAS Registry
    • The DAS Registry. , http://www.dasregistry.org/
  • 46
    • 77954313552 scopus 로고    scopus 로고
    • Archive Ensembl
    • Archive Ensembl. , http://Mar2010.archive.ensembl.org/Mus_musculus/Location/Genome
  • 47
    • 67249117049 scopus 로고    scopus 로고
    • Potential etiologic and functional implications of genome-wide association loci for human diseases and traits
    • 10.1073/pnas.0903103106, 2687147, 19474294
    • Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci USA 2009, 106(23):9362-9367. 10.1073/pnas.0903103106, 2687147, 19474294.
    • (2009) Proc Natl Acad Sci USA , vol.106 , Issue.23 , pp. 9362-9367
    • Hindorff, L.A.1    Sethupathy, P.2    Junkins, H.A.3    Ramos, E.M.4    Mehta, J.P.5    Collins, F.S.6    Manolio, T.A.7
  • 49
    • 77954313448 scopus 로고    scopus 로고
    • Ensembl Variation
    • Ensembl Variation. , http://Mar2010.archive.ensembl.org/info/docs/variation/index.html
  • 52
    • 21444450493 scopus 로고    scopus 로고
    • Perlegen sciences, inc
    • 10.1517/14622416.6.4.439, 16004563
    • Peacock E, Whiteley P. Perlegen sciences, inc. Pharmacogenomics 2005, 6(4):439-442. 10.1517/14622416.6.4.439, 16004563.
    • (2005) Pharmacogenomics , vol.6 , Issue.4 , pp. 439-442
    • Peacock, E.1    Whiteley, P.2
  • 53
    • 84896460887 scopus 로고    scopus 로고
    • Genome Reference Consortium
    • Genome Reference Consortium. , http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/index.shtml
  • 54
    • 77954314145 scopus 로고    scopus 로고
    • Ensembl 57: Region in Detail (IL2)
    • Ensembl 57: Region in Detail (IL2). , http://Mar2010.archive.ensembl.org/Homo_sapiens/Location/View?r=4:123371793-123378703
  • 55
    • 77954309744 scopus 로고    scopus 로고
    • Ensembl 57: Genomic Alignments (IL2)
    • Ensembl 57: Genomic Alignments (IL2). , http://Mar2010.archive.ensembl.org/Homo_sapiens/Gene/Compara_Alignments?align=457&db=core&g=ENSG00000109471&r=4%3A123372630-123377650&t=ENST00000226730
  • 56
    • 33747881750 scopus 로고    scopus 로고
    • The general transcription machinery and general cofactors
    • 10.1080/10409230600648736, 16858867
    • Thomas MC, Chiang CM. The general transcription machinery and general cofactors. Crit Rev Biochem Mol Biol 2006, 41(3):105-178. 10.1080/10409230600648736, 16858867.
    • (2006) Crit Rev Biochem Mol Biol , vol.41 , Issue.3 , pp. 105-178
    • Thomas, M.C.1    Chiang, C.M.2
  • 57
    • 0023821516 scopus 로고
    • Identification of a putative regulator of early T cell activation genes
    • 10.1126/science.3260404, 3260404
    • Shaw JP, Utz PJ, Durand DB, Toole JJ, Emmel EA, Crabtree GR. Identification of a putative regulator of early T cell activation genes. Science 1988, 241(4862):202-205. 10.1126/science.3260404, 3260404.
    • (1988) Science , vol.241 , Issue.4862 , pp. 202-205
    • Shaw, J.P.1    Utz, P.J.2    Durand, D.B.3    Toole, J.J.4    Emmel, E.A.5    Crabtree, G.R.6
  • 58
    • 77954313697 scopus 로고    scopus 로고
    • Ensembl 57: Gene Tree (MYO6)
    • Ensembl 57: Gene Tree (MYO6). , http://Mar2010.archive.ensembl.org/Homo_sapiens/Gene/Compara_Tree?g=ENSG00000196586
  • 59
    • 84870438764 scopus 로고    scopus 로고
    • Gene Ontology
    • Gene Ontology. , http://www.geneontology.org/GO.evidence.shtml
  • 60
    • 77954316097 scopus 로고    scopus 로고
    • Ensembl 57: Region in Detail (MYO6)
    • Ensembl 57: Region in Detail (MYO6). , http://Mar2010.archive.ensembl.org/Homo_sapiens/Location/View?db=core;g=ENSG00000196586;t=ENST00000428345;r=6:76441551-76501760
  • 61
    • 77954316470 scopus 로고    scopus 로고
    • Ensembl 57: Region in Detail (mouse IL2)
    • Ensembl 57: Region in Detail (mouse IL2). , http://Mar2010.archive.ensembl.org/Mus_musculus/Location/View?r=3:37018158-37039973
  • 62
    • 77954309955 scopus 로고    scopus 로고
    • Ensembl 57: Phenotype Data (rs2476601)
    • Ensembl 57: Phenotype Data (rs2476601). , http://Mar2010.archive.ensembl.org/Homo_sapiens/Variation/Phenotype?r=1:114372569-114382568;v=rs2476601;vdb=variation;vf=13431890
  • 63
    • 77954311944 scopus 로고    scopus 로고
    • Ensembl 57: Region in Detail (PTPN22)
    • Ensembl 57: Region in Detail (PTPN22). , http://Mar2010.archive.ensembl.org/Homo_sapiens/Location/View?r=1:114372569-114382568;v=rs2476601;vdb=variation;vf=13431890


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.