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]  Andrew R. Jones,et al.  ProteomeXchange provides globally co-ordinated proteomics data submission and dissemination , 2014, Nature Biotechnology.

[2]  Robert D. Finn,et al.  Rfam 12.0: updates to the RNA families database , 2014, Nucleic Acids Res..

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

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

[5]  David Fenyö,et al.  Informatics and data management in proteomics. , 2002, Trends in biotechnology.

[6]  E. Boerwinkle,et al.  dbNSFP v2.0: A Database of Human Non‐synonymous SNVs and Their Functional Predictions and Annotations , 2013, Human mutation.

[7]  David Haussler,et al.  The UCSC Genome Browser database: 2014 update , 2013, Nucleic Acids Res..

[8]  Alejandro A. Schäffer,et al.  WindowMasker: window-based masker for sequenced genomes , 2006, Bioinform..

[9]  Susumu Goto,et al.  Data, information, knowledge and principle: back to metabolism in KEGG , 2013, Nucleic Acids Res..

[10]  International Human Genome Sequencing Consortium.  Finishing the euchromatic sequence of the human genome , 2004 .

[11]  Kenny Q. Ye,et al.  An integrated map of genetic variation from 1,092 human genomes , 2012, Nature.

[12]  D. Cooper,et al.  Human Gene Mutation Database , 1996, Human Genetics.

[13]  David Haussler,et al.  Computational reconstruction of ancestral DNA sequences. , 2008, Methods in molecular biology.

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

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

[16]  Mary Goldman,et al.  The UCSC Genome Browser database: extensions and updates 2011 , 2011, Nucleic Acids Res..

[17]  M. Frommer,et al.  CpG islands in vertebrate genomes. , 1987, Journal of molecular biology.

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

[19]  Yun Sung Cho,et al.  Minke whale genome and aquatic adaptation in cetaceans , 2013, Nature Genetics.

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

[21]  David Haussler,et al.  The UCSC genome browser database: update 2007 , 2006, Nucleic Acids Res..

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

[23]  David Haussler,et al.  HAL: a hierarchical format for storing and analyzing multiple genome alignments , 2013, Bioinform..

[24]  Bronwen L. Aken,et al.  GENCODE: The reference human genome annotation for The ENCODE Project , 2012, Genome research.

[25]  Laurent Gil,et al.  Ensembl 2013 , 2012, Nucleic Acids Res..

[26]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[27]  Mary Goldman,et al.  The UCSC Genome Browser database: extensions and updates 2013 , 2012, Nucleic Acids Res..

[28]  James C. Mullikin,et al.  A Defined Zebrafish Line for High-Throughput Genetics and Genomics: NHGRI-1 , 2014, Genetics.

[29]  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.

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

[31]  I. Dubchak,et al.  Visualizing genomes: techniques and challenges , 2010, Nature Methods.

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

[33]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[34]  The Uniprot Consortium,et al.  UniProt: a hub for protein information , 2014, Nucleic Acids Res..

[35]  S. Batalov,et al.  A gene atlas of the mouse and human protein-encoding transcriptomes. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[36]  Daniel R. Zerbino,et al.  Ensembl 2014 , 2013, Nucleic Acids Res..

[37]  Melissa J. Landrum,et al.  RefSeq: an update on mammalian reference sequences , 2013, Nucleic Acids Res..

[38]  S. Eddy,et al.  tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. , 1997, Nucleic acids research.

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

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

[41]  Daniel Rios,et al.  Bioinformatics Applications Note Databases and Ontologies Deriving the Consequences of Genomic Variants with the Ensembl Api and Snp Effect Predictor , 2022 .

[42]  Jun S. Liu,et al.  The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans , 2015, Science.

[43]  David Haussler,et al.  The Human Epigenome Browser at Washington University , 2011, Nature Methods.

[44]  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.

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

[46]  Terrence S. Furey,et al.  The UCSC Genome Browser Database: update 2006 , 2005, Nucleic Acids Res..

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

[48]  Evan Bolton,et al.  Database resources of the National Center for Biotechnology Information , 2017, Nucleic Acids Res..

[49]  Adam C. Siepel,et al.  PHAST and RPHAST: phylogenetic analysis with space/time models , 2011, Briefings Bioinform..

[50]  David S. Goodsell,et al.  The RCSB Protein Data Bank: views of structural biology for basic and applied research and education , 2014, Nucleic Acids Res..

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

[52]  G. Benson,et al.  Tandem repeats finder: a program to analyze DNA sequences. , 1999, Nucleic acids research.

[53]  Brian J. Raney,et al.  Elephant shark genome provides unique insights into gnathostome evolution , 2014, Nature.

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

[55]  Eric W. Deutsch,et al.  The PeptideAtlas project , 2005, Nucleic Acids Res..

[56]  S. Gabriel,et al.  Analysis of 6,515 exomes reveals a recent origin of most human protein-coding variants , 2012, Nature.

[57]  D. Haussler,et al.  Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[58]  G. Hong,et al.  Nucleic Acids Research , 2015, Nucleic Acids Research.

[59]  Sean R. Davis,et al.  NCBI GEO: archive for functional genomics data sets—update , 2012, Nucleic Acids Res..

[60]  Jeffrey R. Whiteaker,et al.  Proteogenomic characterization of human colon and rectal cancer , 2014, Nature.

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

[62]  Peter Schattner,et al.  The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs , 2005, Nucleic Acids Res..

[63]  D. Haussler,et al.  Ultraconserved Elements in the Human Genome , 2004, Science.

[64]  Jonathan M. Mudge,et al.  The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. , 2009, Genome research.

[65]  K. Pollard,et al.  Detection of nonneutral substitution rates on mammalian phylogenies. , 2010, Genome research.

[66]  Cesare Furlanello,et al.  A promoter-level mammalian expression atlas , 2014, Nature.

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

[68]  L. B. Snoek,et al.  Remarkably Divergent Regions Punctuate the Genome Assembly of the Caenorhabditis elegans Hawaiian Strain CB4856 , 2015, Genetics.

[69]  D. Karolchik,et al.  The UCSC Genome Browser database: 2016 update , 2015, bioRxiv.

[70]  A. Nekrutenko,et al.  Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences , 2010, Genome Biology.

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

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

[73]  Nicolas Altemose,et al.  Centromere reference models for human chromosomes X and Y satellite arrays , 2013, Genome research.

[74]  Heidi L Rehm,et al.  ClinGen--the Clinical Genome Resource. , 2015, The New England journal of medicine.

[75]  J. Bonfield,et al.  Finishing the euchromatic sequence of the human genome , 2004, Nature.

[76]  Philip Cayting,et al.  An encyclopedia of mouse DNA elements (Mouse ENCODE) , 2012, Genome Biology.

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

[78]  Ting Wang,et al.  Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser , 2013, Bioinform..

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

[80]  David Haussler,et al.  Cactus: Algorithms for genome multiple sequence alignment. , 2011, Genome research.

[81]  D. Karolchik,et al.  The UCSC Genome Browser database: 2017 update , 2016, Nucleic Acids Res..

[82]  David L. Wheeler,et al.  GenBank , 2015, Nucleic Acids Res..

[83]  Hiroyuki Ogata,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..

[84]  Philip L. F. Johnson,et al.  A Draft Sequence of the Neandertal Genome , 2010, Science.

[85]  Casey M. Bergman,et al.  Annotating genes and genomes with DNA sequences extracted from biomedical articles , 2011, Bioinform..

[86]  Obi L. Griffith,et al.  ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation , 2006, Bioinform..

[87]  E. Birney,et al.  Pfam: the protein families database , 2013, Nucleic Acids Res..

[88]  Tim J. P. Hubbard,et al.  Dalliance: interactive genome viewing on the web , 2011, Bioinform..

[89]  Philip Lijnzaad,et al.  The Ensembl genome database project , 2002, Nucleic Acids Res..

[90]  P. Stenson,et al.  The Human Gene Mutation Database: 2008 update , 2009, Genome Medicine.

[91]  Jeroen F. J. Laros,et al.  LOVD v.2.0: the next generation in gene variant databases , 2011, Human mutation.

[92]  Gonçalo R. Abecasis,et al.  The variant call format and VCFtools , 2011, Bioinform..

[93]  Jie Wang,et al.  Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium , 2012, Nucleic Acids Res..

[94]  Eric W Deutsch,et al.  The state of the human proteome in 2012 as viewed through PeptideAtlas. , 2013, Journal of proteome research.

[95]  Adrian W. Briggs,et al.  A High-Coverage Genome Sequence from an Archaic Denisovan Individual , 2012, Science.

[96]  Katherine S. Pollard,et al.  A Model-Based Analysis of GC-Biased Gene Conversion in the Human and Chimpanzee Genomes , 2013, PLoS genetics.

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

[98]  Rachel S. G. Sealfon,et al.  Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak , 2014, Science.

[99]  David Haussler,et al.  Using native and syntenically mapped cDNA alignments to improve de novo gene finding , 2008, Bioinform..

[100]  R. Wilson,et al.  Modernizing Reference Genome Assemblies , 2011, PLoS biology.

[101]  David Haussler,et al.  The UCSC Ebola Genome Portal , 2014, PLoS currents.

[102]  David Haussler,et al.  The UCSC Known Genes , 2006, Bioinform..

[103]  ENCODEConsortium,et al.  An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.

[104]  David Haussler,et al.  ENCODE Data in the UCSC Genome Browser: year 5 update , 2012, Nucleic Acids Res..

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

[106]  P. Stenson,et al.  Human Gene Mutation Database (HGMD , 2003 .

[107]  David Haussler,et al.  Comparative assembly hubs: Web-accessible browsers for comparative genomics , 2013, Bioinform..

[108]  David Haussler,et al.  Navigating protected genomics data with UCSC Genome Browser in a Box , 2014, Bioinform..

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

[110]  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.

[111]  A. Smit.  Interspersed repeats and other mementos of transposable elements in mammalian genomes. , 1999, Current opinion in genetics & development.

[112]  L. Stein,et al.  Annotating Cancer Variants and Anti-Cancer Therapeutics in Reactome , 2012, Cancers.

[113]  Henning Hermjakob,et al.  The Reactome pathway knowledgebase , 2013, Nucleic Acids Res..

[114]  Mario Stanke,et al.  Gene prediction with a hidden Markov model and a new intron submodel , 2003, ECCB.

[115]  S. Karlin,et al.  Prediction of complete gene structures in human genomic DNA. , 1997, Journal of molecular biology.

[116]  Ewen Callaway,et al.  Global genomic data-sharing effort kicks off , 2014, Nature.

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

[118]  Sean R. Eddy,et al.  Rfam 11.0: 10 years of RNA families , 2012, Nucleic Acids Res..

[119]  Robert S. Harris,et al.  Improved pairwise alignment of genomic dna , 2007 .

[120]  Jon W. Huss,et al.  BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources , 2009, Genome Biology.

[121]  G. Bejerano,et al.  GREAT improves functional interpretation of cis-regulatory regions , 2010, Nature Biotechnology.

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

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

[124]  The UniProt Consortium,et al.  Update on activities at the Universal Protein Resource (UniProt) in 2013 , 2012, Nucleic Acids Res..

[125]  Albert J. Vilella,et al.  A high-resolution map of human evolutionary constraint using 29 mammals , 2011, Nature.

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

[127]  Peggy Hall,et al.  The NHGRI GWAS Catalog, a curated resource of SNP-trait associations , 2013, Nucleic Acids Res..

[128]  Deanna M. Church,et al.  ClinVar: public archive of relationships among sequence variation and human phenotype , 2013, Nucleic Acids Res..

[129]  Huaiyu Mi,et al.  The InterPro protein families database: the classification resource after 15 years , 2014, Nucleic Acids Res..

[130]  Galt P. Barber,et al.  BigWig and BigBed: enabling browsing of large distributed datasets , 2010, Bioinform..

[131]  Eric S. Lander,et al.  An Improved Canine Genome and a Comprehensive Catalogue of Coding Genes and Non-Coding Transcripts , 2014, PloS one.

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

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

[134]  David Haussler,et al.  The UCSC genome browser and associated tools , 2012, Briefings Bioinform..

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

[136]  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.

[137]  Philip L. F. Johnson,et al.  Genetic history of an archaic hominin group from Denisova Cave in Siberia , 2010, Nature.

[138]  T. Mikkelsen,et al.  The NIH Roadmap Epigenomics Mapping Consortium , 2010, Nature Biotechnology.

[139]  Thomas Lengauer,et al.  BLUEPRINT to decode the epigenetic signature written in blood , 2012, Nature Biotechnology.

[140]  Jim Thurmond,et al.  FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations , 2014, Nucleic Acids Res..

[141]  Yong-shu He,et al.  [Structural variation in the human genome]. , 2009, Yi chuan = Hereditas.

[142]  Patricia P. Chan,et al.  GtRNAdb: a database of transfer RNA genes detected in genomic sequence , 2008, Nucleic Acids Res..