title: Touring Ensembl: a practical guide to genome browsing.
abstract: The number of databases in molecular biological fields has rapidly increased to provide a large-scale resource. Though valuable information is available, data can be difficult to access, compare and integrate due to different formats and presentations of web interfaces. This paper offers a practical guide to the integration of gene, comparative genomic, and functional genomics data using the Ensembl website at http://www.ensembl.org.The Ensembl genome browser and underlying databases focus on chordate organisms. More species such as plants and microorganisms can be investigated using our sister browser at http://www.ensemblgenomes.org.In this study, four examples are used that sample many pages and features of the Ensembl browser. We focus on comparative studies across over 50 mostly chordate organisms, variations linked to disease, functional genomics, and access of external information housed in databases outside the Ensembl project. Researchers will learn how to go beyond simply exporting one gene sequence, and explore how a genome browser can integrate data from various sources and databases to build a full and comprehensive biological picture.
authors.affiliation: European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK.
authors.forename: Giulietta M
authors.initials: GM
authors.lastname: Spudich
authors.forename: Xosé M
authors.initials: XM
authors.lastname: Fernández-Suárez
mesh_terms: D000818:Animals; D001483:Base Sequence; D017124:Conserved Sequence; D030541:Databases, Genetic; D023281:Genomics / Q000379:methods*; D006801:Humans; D007376:Interleukin-2 / Q000235:genetics; D020407:Internet; D051379:Mice; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide; D051381:Rats; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics; D014584:User-Computer Interface
chemical_list: D007376:Interleukin-2
references.citation: Nat Genet. 2004 Aug;36(8):867-71
references.pmid: 15235602
references.citation: Nature. 1986 May 15-21;321(6067):209-13
references.pmid: 2423876
references.citation: Methods Enzymol. 2002;350:469-83
references.pmid: 12073330
references.citation: Nucleic Acids Res. 2005 Jan 1;33(Database issue):D154-9
references.pmid: 15608167
references.citation: J Cell Biol. 2005 Jan 17;168(2):329-38
references.pmid: 15657400
references.citation: Dev Biol. 1999 Oct 15;214(2):331-41
references.pmid: 10525338
references.citation: Cell. 2007 May 18;129(4):823-37
references.pmid: 17512414
references.citation: Genome Res. 2005 Jul;15(7):901-13
references.pmid: 15965027
references.citation: Hum Mol Genet. 2007 Feb 1;16(3):343-54
references.pmid: 17210670
references.citation: Nat Methods. 2007 Aug;4(8):651-7
references.pmid: 17558387
references.citation: Cell. 2007 Mar 23;128(6):1231-45
references.pmid: 17382889
references.citation: Biochim Biophys Acta. 1994 Mar 1;1217(2):235-8
references.pmid: 8110843
references.citation: Genome Res. 2002 Mar;12(3):458-61
references.pmid: 11875034
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D1-4
references.pmid: 19033364
references.citation: Cell. 2006 Jul 28;126(2):375-87
references.pmid: 16873067
references.citation: Genomics. 1992 Aug;13(4):1095-107
references.pmid: 1505946
references.citation: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D68-73
references.pmid: 16381958
references.citation: Nature. 2007 Jun 14;447(7146):799-816
references.pmid: 17571346
references.citation: Nucleic Acids Res. 2004 Jan 1;32(Database issue):D258-61
references.pmid: 14681407
references.citation: Proc Natl Acad Sci U S A. 1983 Dec;80(24):7437-41
references.pmid: 6324170
references.citation: Nucleic Acids Res. 2007 Jan;35(Database issue):D61-5
references.pmid: 17130148
references.citation: BMC Bioinformatics. 2001;2:7
references.pmid: 11667947
references.citation: Genome Res. 2009 Feb;19(2):327-35
references.pmid: 19029536
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D5-15
references.pmid: 18940862
references.citation: Proc Natl Acad Sci U S A. 2009 Jun 9;106(23):9362-7
references.pmid: 19474294
references.citation: Pharmacogenomics. 2005 Jun;6(4):439-42
references.pmid: 16004563
references.citation: BMC Genomics. 2010 May 11;11:293
references.pmid: 20459805
references.citation: Nat Genet. 2000 May;25(1):25-9
references.pmid: 10802651
references.citation: Nat Genet. 2001 Dec;29(4):412-7
references.pmid: 11726928
references.citation: Science. 1988 Jul 8;241(4862):202-5
references.pmid: 3260404
references.citation: Curr Biol. 1999 Sep 9;9(17):R661-7
references.pmid: 10508580
references.citation: Nucleic Acids Res. 2009 Jul;37(Web Server issue):W23-7
references.pmid: 19420058
references.citation: Nature. 2007 Apr 5;446(7136):685-9
references.pmid: 17377532
references.citation: BMC Genomics. 2009 Jan 14;10:22
references.pmid: 19144180
references.citation: Brief Funct Genomic Proteomic. 2007 Sep;6(3):202-19
references.pmid: 17967807
references.citation: Bioinformatics. 2009 May 1;25(9):1189-91
references.pmid: 19151095
references.citation: Curr Protoc Bioinformatics. 2010 Jun;Chapter 1:1.15.1-1.15.48
references.pmid: 20521244
references.citation: Crit Rev Biochem Mol Biol. 2006 May-Jun;41(3):105-78
references.pmid: 16858867
references.citation: Genome Res. 2004 Jan;14(1):160-9
references.pmid: 14707178
references.citation: Nature. 2007 Oct 18;449(7164):851-61
references.pmid: 17943122
references.citation: Trends Genet. 2001 Sep;17(9):520-7
references.pmid: 11525835
references.citation: Genome Biol. 2003;5(1):R1
references.pmid: 14709173
references.citation: Curr Opin Immunol. 1995 Jun;7(3):333-42
references.pmid: 7546397