GeneCards - genome-wide gene and disease databases
The GeneCards® database of human genes was launched in 1997, and has expanded since then to encompass gene-centric, disease-centric, and pathway-centric entities and relationships within the GeneCards Suite, effectively navigating the universe of human biological data - genes, proteins, cells, regulatory elements, biological pathways, and diseases - and the connections amongst them. The Suite’s integrated biomedical knowledgebase includes GeneCards, the integrated human gene database, MalaCards, the unified human disease database, PathCards, the consolidated human pathways database, and GeneLoc, the human genomic neighborhood location-based database. The Suite newest members, focusing on the emerging field of annotating the non-coding genomic “dark matter”, are GeneHancer, an innovative regulatory element database with ~400,000 enhancer and promoter entries, and GeneCaRNA, an all-inclusive gene-centric ncRNA database with ~220,000 ncRNA gene pages.
The knowledgebase amalgamates information from >150 selected sources related to genes, proteins, ncRNAs, regulatory elements, chemical compounds, drugs, splice variants, SNPs, signaling molecules, differentiation protocols, biological pathways, stem cells, genetic tests, clinical trials, diseases, publications, and more, and empowers Next Generation Sequencing (NGS) analysis by highlighting associations between genes and phenotypes, providing supporting evidence for immediate evaluation via the Suite’s NGS analysis tool VarElect, the phenotype interpreter. VarElect accepts a list of genes and phenotypes as input, and computes prioritized direct (keyword-based) and indirect (inferred from gene-to-gene associations) gene/disease connections. Rounding out the Suite are GeneAnalytics, for gene set enrichment analysis, GenesLikeMe, for finding genes with shared descriptors, and GeneALaCart, for batch queries.
The Suite’s websites, data dumps, APIs, publications, and collaborations are enjoyed by about 6 million users, including research and applied scientists, doctors, geneticists, and lay-people, in >3,000 institutions worldwide, encompassing academia, national patent offices, leading biopharma and diagnostic companies, and hospitals.
Selected GeneCards Suite Publications
- GeneCards – the human gene database
www.genecards.org
Stelzer G, Rosen R, Plaschkes I, Zimmerman S, Twik M, Fishilevich S, Iny Stein T, Nudel R, Lieder I, Mazor Y, Kaplan S, Dahary D, Warshawsky D, Guan - Golan Y, Kohn A, Rappaport N, Safran M, and Lancet D. The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analysis , Current Protocols in Bioinformatics(2016), 54:1.30.1 - 1.30.33.doi: 10.1002 / cpbi.5. [PDF] - MalaCards – the human disease database
www.malacards.org
Rappaport N, Twik M, Plaschkes I, Nudel R, Iny Stein T, Levitt J, Gershoni M, Morrey CP, Safran M, and Lancet D. MalaCards: an amalgamated human disease compendium with diverse clinical and genetic annotation and structured search , Nucleic Acids Research(2016), doi: 10.1093 / nar / gkw1012. [PDF] - GeneCaRNA – The Human ncRNA Database
www.genecards.org/genecarna
Barshir R, Fishilevich F, Iny-Stein T, Zelig O, Mazor Y, Guan-Golan Y, Safran M, Lancet D. GeneCaRNA: a comprehensive gene-centric database of human non-coding RNAs in the GeneCards Suite, Journal of Molecular Biology (2021), 433 (11), p.166913, 10.1016/j.jmb.2021.166913 [PDF] - GeneHancer – the human database of regulatory elements and their target genes
www.genecards.org
Fishilevich S, Nudel R, Rappaport N, Hadar R, Plaschkes I, Iny Stein T, Rosen N, Kohn A, Twik M, Safran M, Lancet D, and Cohen D. GeneHancer: genome - wide integration of enhancers and target genes in GeneCards , Database(Oxford)(2017), doi: 10.1093 / database / bax028. [PDF] - VarElect – the NGS phenotyper
ve.genecards.org
Stelzer G, Plaschkes I, Oz - Levi D, Alkelai A, Olender T, Zimmerman S, Twik M., Belinky F, Fishilevich S, Nudel R, Guan - Golan Y, Warshawsky D, Dahary D, Kohn A, Mazor Y, Kaplan S, Iny Stein T, Baris H, Rappaport N, Safran M, and Lancet D. VarElect: the phenotype - based variation prioritizer of the GeneCards suite , BMC Genomics(2016), 17(Suppl 2):444; DOI: 10.1186 / s12864 - 016 - 2722 - 2. [PDF] - GeneAnalytics – the gene set analysis tool
ga.genecards.org
Ben-Ari Fuchs S, Lieder I, Stelzer G, Mazor Y, Buzhor E, Kaplan S, Bogoch Y, Plaschkes I, Shitrit A, Rappaport N, Kohn A, Edgar R, Shenhav L, Safran M, Lancet D, Guan-Golan Y, Warshawsky D, and Strichman R. GeneAnalytics:An Integrative Gene Set Analysis Tool for Next Generation Sequencing, RNAseq and Microarray Data, OMICS(2016) Volume 20, Number 3; DOI: 10.1089/omi.2015.0168. [PDF] - PathCards – the pathway unification database
pathcards.genecards.org
Belinky F, Nativ N, Stelzer G, Zimmerman S, Iny Stein T, Safran M, and Lancet, D. PathCards: multi-source consolidation of human biological pathways, Database (2015) Vol. 2015: article ID bav006; doi:10.1093/database/bav006. [PDF] - HIPED – the database of protein abundance in human tissues
www.genecards.org
Fishilevich S, Zimmerman S, Kohn A, Iny Stein T, Safran M, and Lancet D. Genic Insights From Integrated Human Proteomics in GeneCards, Database (2016); doi: 10.1093/database/baw030. [PDF] - GeneLoc – the genome locator
genecards.weizmann.ac.il/geneloc
Rosen, N., Chalifa-Caspi, V., Shmueli, O., Adato, A., Lapidot, M., Stampnitzky, J., Safran, M., and Lancet, D. GeneLoc: Exon-based integration of human genome maps. Bioinformatics: 19,S1: 222-224 (2003) . [PDF] - GeneALaCart – the GeneCards batch-query processor
genealacart.genecards.org
Stelzer G, Rosen R, Plaschkes I, Zimmerman S, Twik M, Fishilevich S, Iny Stein T, Nudel R, Lieder I, Mazor Y, Kaplan S, Dahary D, Warshawsky D, Guan - Golan Y, Kohn A, Rappaport N, Safran M, and Lancet D. The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analysis , Current Protocols in Bioinformatics(2016), 54:1.30.1 - 1.30.33.doi: 10.1002 / cpbi.5. [PDF] - GenesLikeMe – the partner hunter
glm.genecards.org
Stelzer G, Inger A, Olender T, Iny Stein T, Dalah I, Harel A, Safran M and Lancet D. GeneDecks: paralog hunting and gene-set distillation with GeneCards annotation OMICS, 2009, 13(6): 477-487 [PDF]