GeneCards Version 3: the human gene integrator

By M. Safran, Irina Dalah, J. Alexander, Naomi Rosen, Tsippi Iny Stein, M. Shmoish, N. Nativ, Iris Bahir, T. Doniger, H. Krug and 6 more. Database J. Biol. Databases Curation, 2010

1,913 citations recorded by the source corpus.

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

View Paper: https://www.semanticscholar.org/paper/9685f3a1f5a50e175e2078a45a558265ef66cde3

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Citations in the corpus

The Human Urine Metabolome (2013, background): “Each MetaboCard entry contains up to 120 data fields many of which are hyperlinked to other databases (KEGG [45], PubChem [46], MetaCyc [47], ChEBI [48], PDB [49], UniProt [50], and GenBank [51] as well as to GeneCard IDs [52], GeneAtlas IDs [53] and HGNC IDs [54] for each of the corresponding enzym”
SwissTargetPrediction: a web server for target prediction of bioactive small molecules (2014, background): “The result page lists the predicted targets with their common name together with links to GeneCards (30) (for human proteins), UniProt (31) and ChEMBL (6) databases when available (see Figure 1).”
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored (2010, methodology): “Apart from making the entire SQL database back-end available for download (free for non-proﬁt institutions), this is mainly achieved via the following routes: First, the database maintains mutual HTML cross-references with a number of widely used websites, including UniProt (48), SMART (49), GeneCar”
dbSUPER: a database of super-enhancers in mouse and human genome (2015, background): “Further, dbSUPER provides external links to UCSC Genome Browser (43) (http://genome.ucsc.edu/), NCBI Gene (44, 45) (http://www.ncbi.nlm.nih.gov/gene/), GeneCards (46) (http://www.genecards.org), UniProt (47) (http://uniprot.org) and Wikipedia (http://en.wikipedia.org) to facilitate users to use thos”
DrugBank 3.0: a comprehensive resource for ‘Omics’ research on drugs (2010, background): “For instance, version 2.0 of DrugBank contained up to 18 database hyperlinks in every DrugCard entry, including links to KEGG (9), PubChem (7), ChEBI (10), PharmGKB (6), PDB (18), GenBank (19), DIN, RxList, PDRhealth, Wikipedia, ATC, UniProt (16), Pfam (20), dbSNP (17), GeneCards (21), GenAtlas (22)”
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins (2016, background): “GeneCards (8) is becoming one of the most comprehensive resources for collective knowledge about genes and proteins, aggregating information from over 120 resources.”
The Human Gene Mutation Database (HGMD) and Its Exploitation in the Fields of Personalized Genomics and Molecular Evolution (2012, methodology): “Links to GenAtlas (Fr´ezal, 1998), the HUGO Nomenclature Committee (Seal et al., 2011), GeneCards (Safran et al., 2010), GeneTests-GeneClinics (Pagon, 2006), Entrez Gene (Maglott et al., 2011), UniProt (UniProt Consortium, 2012), JSNP (Hirakawa, 2002), COSMIC (Forbes et al., 2010), and the Genetic…”
ALKBH5 Is a Mammalian RNA Demethylase that Impacts RNA Metabolism and Mouse Fertility (2012, unknown): “We sorted the differentially expressed transcripts with reference to a compiled data set of reported spermatogenesis/infertility-related genes (Ashburner et al., 2000; Consortium, 2012; He et al., 2007; Pang et al., 2006; Rockett et al., 2004; Rossi et al., 2004; Safran et al., 2010; Shaha et al., 2”
Massive mining of publicly available RNA-seq data from human and mouse (2017, background): “Such data can complement tissue and cell line expression resources such as BioGPS 35 and GTEx 14 as well as resources that provide accumulated knowledge about genes and proteins such as GeneCards 36 , the Harmonizome 37 , and the NCBI gene data-base 38 .”
The UCSC Genome Browser (2003, unknown): “…Genes track ( Maglott et al., 2011 ) ( Sayers et al., 2011 ), Ensembl Genes ( Flicek et al., 2011 ), GeneLynx ( Lenhard et al., 2001 ), GeneCards ( Safran et al., 2010 ), AceView, PubMed ( Sayers et al., 2011 ; UNIT 1.3), the HUGO Gene Nomenclature Committee Database (HGNC; Seal et al., 2011 ),…”
PATRIC: the Comprehensive Bacterial Bioinformatics Resource with a Focus on Human Pathogenic Species (2011, background): “Both the “Genetic Association Source” and the “Comparative Toxicogenomics Source” provide additional information about the human genes from NCBI as well as GeneCards, a comprehensive and authoritative compendium of annotative information pertaining to human genes (35).”