GeneCards Version 3: the human gene integrator.
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.
Safran
Marilyn
M
Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel. marilyn.safran@weizmann.ac.il
Dalah
Irina
I
Alexander
Justin
J
Rosen
Naomi
N
Iny Stein
Tsippi
T
Shmoish
Michael
M
Nativ
Noam
N
Bahir
Iris
I
Doniger
Tirza
T
Krug
Hagit
H
Sirota-Madi
Alexandra
A
Olender
Tsviya
T
Golan
Yaron
Y
Stelzer
Gil
G
Harel
Arye
A
Lancet
Doron
D
D017398:Alternative Splicing; D030541:Databases, Genetic; D030562:Databases, Protein; D015870:Gene Expression; D053263:Gene Regulatory Networks; D030342:Genetic Diseases, Inborn / Q000235:genetics; D015894:Genome, Human; D006801:Humans; D020407:Internet; D009154:Mutation; D020641:Polymorphism, Single Nucleotide; D025941:Protein Interaction Mapping; D057386:Search Engine