The UCSC Genome Browser Database: 2008 update

The University of California, Santa Cruz, Genome Browser Database (GBD) provides integrated sequence and annotation data for a large collection of vertebrate and model organism genomes. Seventeen new assemblies have been added to the database in the past year, for a total coverage of 19 vertebrate and 21 invertebrate species as of September 2007. For each assembly, the GBD contains a collection of annotation data aligned to the genomic sequence. Highlights of this year's additions include a 28-species human-based vertebrate conservation annotation, an enhanced UCSC Genes set, and more human variation, MGC, and ENCODE data. The database is optimized for fast interactive performance with a set of web-based tools that may be used to view, manipulate, filter and download the annotation data. New toolset features include the Genome Graphs tool for displaying genome-wide data sets, session saving and sharing, better custom track management, expanded Genome Browser configuration options and a Genome Browser wiki site. The downloadable GBD data, the companion Genome Browser toolset and links to documentation and related information can be found at: http://genome.ucsc.edu/.

[1]  Ting Wang,et al.  The UCSC Genome Browser Database: update 2009 , 2008, Nucleic Acids Res..

[2]  Simon C. Potter,et al.  Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls , 2007, Nature.

[3]  David Haussler,et al.  Thousands of human mobile element fragments undergo strong purifying selection near developmental genes , 2007, Proceedings of the National Academy of Sciences.

[4]  Kayla E. Smith,et al.  The ENCODE Project at UC Santa Cruz , 2006, Nucleic Acids Res..

[5]  Andreas Prlic,et al.  Ensembl 2007 , 2006, Nucleic Acids Res..

[6]  D. Conrad,et al.  Global variation in copy number in the human genome , 2006, Nature.

[7]  The Uniprot Consortium,et al.  The Universal Protein Resource (UniProt) , 2006, Nucleic Acids Res..

[8]  E. Eichler,et al.  Linkage disequilibrium and heritability of copy-number polymorphisms within duplicated regions of the human genome. , 2006, American journal of human genetics.

[9]  M. Diekhans,et al.  BIOINFORMATICS ORIGINAL PAPER Genome analysis The UCSC Known Genes , 2022 .

[10]  L. Feuk,et al.  Structural variation in the human genome , 2006, Nature Reviews Genetics.

[11]  K. S. Deshpande,et al.  Human protein reference database—2006 update , 2005, Nucleic Acids Res..

[12]  S. L. Wong,et al.  Towards a proteome-scale map of the human protein–protein interaction network , 2005, Nature.

[13]  H. Lehrach,et al.  A Human Protein-Protein Interaction Network: A Resource for Annotating the Proteome , 2005, Cell.

[14]  D. Haussler,et al.  Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. , 2005, Genome research.

[15]  Yi Zhou,et al.  Mutant-specific gene programs in the zebrafish. , 2005, Blood.

[16]  E. Eichler,et al.  Segmental duplications and copy-number variation in the human genome. , 2005, American journal of human genetics.

[17]  G. Helt,et al.  Transcriptional Maps of 10 Human Chromosomes at 5-Nucleotide Resolution , 2005, Science.

[18]  D. Haussler,et al.  Exploring relationships and mining data with the UCSC Gene Sorter. , 2005, Genome research.

[19]  Tomaso Poggio,et al.  Identification and analysis of alternative splicing events conserved in human and mouse. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[20]  Tatiana Tatusova,et al.  NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins , 2004, Nucleic Acids Res..

[21]  Tatiana A. Tatusova,et al.  NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins , 2004, Nucleic Acids Res..

[22]  David Haussler,et al.  The UCSC Proteome Browser , 2004, Nucleic Acids Res..

[23]  Cathy H. Wu,et al.  The Universal Protein Resource (UniProt) , 2004, Nucleic Acids Res..

[24]  Younes Mokrab,et al.  A genome annotation-driven approach to cloning the human ORFeome , 2004, Genome Biology.

[25]  L. Feuk,et al.  Detection of large-scale variation in the human genome , 2004, Nature Genetics.

[26]  Kenny Q. Ye,et al.  Large-Scale Copy Number Polymorphism in the Human Genome , 2004, Science.

[27]  D. Haussler,et al.  Aligning multiple genomic sequences with the threaded blockset aligner. , 2004, Genome research.

[28]  M. Olivier.  A haplotype map of the human genome. , 2003, Nature.

[29]  M. Olivier.  A haplotype map of the human genome , 2003, Nature.

[30]  Tom H. Pringle,et al.  The human genome browser at UCSC. , 2002, Genome research.

[31]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[32]  Ji Huang,et al.  [Serial analysis of gene expression]. , 2002, Yi chuan = Hereditas.

[33]  R. Strausberg,et al.  Genome and genetic resources from the Cancer Genome Anatomy Project. , 2001, Human molecular genetics.

[34]  K. Kinzler,et al.  Serial Analysis of Gene Expression , 1995, Science.

[35]  William Stafford Noble,et al.  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project , 2007, Nature.

[36]  Pardis C Sabeti,et al.  Common deletion polymorphisms in the human genome , 2006, Nature Genetics.

[37]  D. Conrad,et al.  A high-resolution survey of deletion polymorphism in the human genome , 2006, Nature Genetics.

[38]  K. Frazer,et al.  Common deletions and SNPs are in linkage disequilibrium in the human genome , 2006, Nature Genetics.

[39]  Simon Smyth,et al.  Diabetes and obesity: the twin epidemics , 2006, Nature Medicine.

[40]  BIOINFORMATICS APPLICATIONS NOTE doi:10.1093/bioinformatics/btk027 Databases and ontologies , 2006 .

[41]  The International HapMap Consortium.  A haplotype map of the human genome , 2005 .

[42]  Ryan D. Morin,et al.  The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). , 2004, Genome research.

[43]  Terrence S. Furey,et al.  The UCSC Table Browser data retrieval tool , 2004, Nucleic Acids Res..

[44]  Elizabeth M. Smigielski,et al.  dbSNP: the NCBI database of genetic variation , 2001, Nucleic Acids Res..