GeneCards Version 3: the human gene integrator

被引:1304
作者
Safran, Marilyn [1 ,2 ]
Dalah, Irina [1 ]
Alexander, Justin [1 ]
Rosen, Naomi [1 ]
Stein, Tsippi Iny [1 ]
Shmoish, Michael [1 ,3 ]
Nativ, Noam [1 ]
Bahir, Iris [1 ]
Doniger, Tirza [1 ]
Krug, Hagit [1 ]
Sirota-Madi, Alexandra [1 ,4 ]
Olender, Tsviya [1 ]
Golan, Yaron [5 ]
Stelzer, Gil [1 ]
Harel, Arye [1 ]
Lancet, Doron [1 ]
机构
[1] Weizmann Inst Sci, Dept Mol Genet, IL-76100 Rehovot, Israel
[2] Weizmann Inst Sci, Dept Biol Serv, IL-76100 Rehovot, Israel
[3] Technion Israel Inst Technol, Lorry I Lokey Interdisciplinary Ctr Life Sci & En, Bioinformat Knowledge Unit, Haifa, Israel
[4] Tel Aviv Univ, Sackler Sch Med, IL-69978 Tel Aviv, Israel
[5] Xennex Inc, Cambridge, MA USA
来源
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION | 2010年
关键词
D O I
10.1093/database/baq020
中图分类号
Q [生物科学];
学科分类号
07 ; 0710 ; 09 ;
摘要
GeneCards (www.genecards.org) is a comprehensive, authoritative compendium of annotative information about human genes, widely used for nearly 15 years. Its gene-centric content is automatically mined and integrated from over 80 digital sources, resulting in a web-based deep-linked card for each of >73 000 human gene entries, encompassing the following categories: protein coding, pseudogene, RNA gene, genetic locus, cluster and uncategorized. We now introduce GeneCards Version 3, featuring a speedy and sophisticated search engine and a revamped, technologically enabling infrastructure, catering to the expanding needs of biomedical researchers. A key focus is on gene-set analyses, which leverage GeneCards' unique wealth of combinatorial annotations. These include the GeneALaCart batch query facility, which tabulates user-selected annotations for multiple genes and GeneDecks, which identifies similar genes with shared annotations, and finds set-shared annotations by descriptor enrichment analysis. Such set-centric features address a host of applications, including microarray data analysis, cross-database annotation mapping and gene-disorder associations for drug targeting. We highlight the new Version 3 database architecture, its multi-faceted search engine, and its semi-automated quality assurance system. Data enhancements include an expanded visualization of gene expression patterns in normal and cancer tissues, an integrated alternative splicing pattern display, and augmented multi-source SNPs and pathways sections. GeneCards now provides direct links to gene-related research reagents such as antibodies, recombinant proteins, DNA clones and inhibitory RNAs and features gene-related drugs and compounds lists. We also portray the GeneCards Inferred Functionality Score annotation landscape tool for scoring a gene's functional information status. Finally, we delineate examples of applications and collaborations that have benefited from the GeneCards suite. Database URL: www.genecards.org
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页数:16
相关论文
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