The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses

By Gil Stelzer, Naomi Rosen, I. Plaschkes, Shahar Zimmerman, Michal Twik, Simon Fishilevich, Tsippi Iny Stein, R. Nudel, I. Lieder, Yaron Mazor and 8 more. Current Protocols in Bioinformatics, 2016

4,907 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/4f216abb0b4b84748cf891a6a03da03aac509ee2

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Citations in the corpus

AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences (2023, background): “The impact of the predicted structures is further enhanced by their seamless integration into several core data resources, including PDBe-KB ( 17 ), UniProt ( 6 ), Ensembl ( 16 ), InterPro ( 15 ), Genecards ( 24 ) and MobiDB ( 25 ), among others.”
Genenames.org: the HGNC resources in 2023 (2022, background): “In addition, the HGNC data section may include curator notes and/or links to gene groups curated by the HGNC. HGNC Symbol Reports also provide numerous useful external data links to biomedical resources such as NCBI Gene (5), Ensembl (6) UniProt (7), GeneCards (8), RNAcentral (9), UCSC genome browse”
GeneHancer: genome-wide integration of enhancers and target genes in GeneCards (2017, methodology): “This network has (cid:2) 10 enhancers per gene (Table 2), broadly consistent with the excess of enhancers over genes for the estimated 400 000 human enhancers (10) and (cid:2) 120 000 functional genes [ (cid:2) 20 000 protein coding genes and (cid:2) 100 000 non-coding RNA (ncRNA) genes (51)].”
Genenames.org: the HGNC and VGNC resources in 2019 (2018, background): “HGNC symbols are displayed in all major databases containing human gene and protein data including Ensembl (1), NCBI Gene (2), UniProt (3), GeneCards (4) and the UCSC genome browser (5), as well as resources focused on human disease and phenotypes such as Decipher (6), OMIM (7), Locus Reference Geno”
RNAcentral 2021: secondary structure integration, improved sequence search and new member databases (2020, background): “GeneCards (21) and MalaCards (22) have also been included into RNAcentral.”
WikiPathways 2024: next generation pathway database (2023, background): “Additionally, an increasing number of biological databases directly link to WikiPathways content, for example, links from the gene entries at GeneCards as of May 2022 ( 7 ).”
Integration of the Drug–Gene Interaction Database (DGIdb 4.0) with open crowdsource efforts (2020, background): “Previously, DGIdb has been integrated with other community resources such as GeneCards(24), which uses DGIdb as a source for interactions between GeneCards gene entries and drugs, and BioGPS(25), which offers a DGIdb plug-in for searching drug-gene interactions.”
Identification of genetic elements in metabolism by high-throughput mouse phenotyping (2018, neutral): “Literature information on the function of the resulting list of genes was inspected using PubMed, LitInspector 48 , and Gen-eCards 49 .”
MalaCards: an amalgamated human disease compendium with diverse clinical and genetic annotation and structured search (2016, methodology): “This is accomplished by employing sophisticated data-mining strategies modelled after the widely-used GeneCards database (2,3).”
Genenames.org: the HGNC and VGNC resources in 2021 (2020, background): “HGNC nomenclature data is displayed by many external resources including NCBI Gene (7), Ensembl (8), UniProt (9), GeneCards (10), RNAcentral (11) and the UCSC genome browser (12), as well as resources focused on human disease and phenotypes such as Decipher (13), OMIM (14), ClinGen (15), ClinVar (16”
HERB: a high-throughput experiment- and reference-guided database of traditional Chinese medicine (2020, methodology): “We further standardized gene names for the newly curated TCM targets according to the NCBI nomenclature and GeneCards database (37), and then cross-referenced them with the TTD database (17), a widely used therapeutic target database for modern compounds.”
The UCSC Genome Browser database: 2017 update (2016, methodology): “Other changes for the gene description page include updated data and links to the MalaCards human disease database (39) and updated Wikipedia links.”