| Content | |
|---|---|
| Data types captured | Human genes and model orthologues |
| Organisms | Homo sapiens |
| Contact | |
| Research center | Crown Human Genome Center, WIS |
| Primary citation | PMID 27322403 |
| Access | |
| Data format | HTML |
| Website | www |
GeneCards is a database of human genes, which provides genomic, proteomic, transcriptomic, genetic, medical, and functional information on all known and predicted human genes. It is developed and maintained by the Crown Human Genome Center at the Weizmann Institute of Science, in collaboration with LifeMap Sciences.
The database provides a comprehensive view of the current available biomedical information about the searched gene, including its aliases and identifiers, the encoded proteins, associated diseases and variations, its function, relevant publications and more. The GeneCards database provides access to free Web resources about more than 466,000 known and predicted human genes, integrated from >190 data resources, such as HGNC, Ensembl, and NCBI. The core gene list is based on approved gene symbols published by the HUGO Gene Nomenclature Committee (HGNC), and on NCBI and Ensembl. The information is carefully gathered and selected from these databases by sophisticated integration algorithms. Each gene record is subsequently annotated with information from >190 sources, presented in relevant GeneCards pages, and empowering complex user search queries.
Over time, the GeneCards database has developed a suite of tools, as described below, which have more specialized capabilities leveraging the database. Since 1998, the GeneCards Suite has been widely used by bioinformatics, genomics and medical communities well into the 21st century.
History
Since the 1980s, sequence information has become increasingly abundant; subsequently many laboratories realized this and began to store such information in central repositories-the primary database. However, the information provided by the primary sequence databases (lower level databases) focus on different aspects. To gather these scattered data, the Weizmann Institute of Science's Crown Human Genome Centre developed a database called ‘GeneCards’ in 1997. This database mainly dealt with human genome information, human genes, the encoded proteins’ functions, and related diseases, though it has expanded since that time.
Growth
Initially, the GeneCards database had two main features: delivery of integrated biomedical information for a gene in ‘card’ format, and a text-based search engine. Since 1998, the database has integrated more data resources and data types, such as protein expression and gene network information. It has also improved the speed and sophistication of the search engine, and expanded from a gene-centric dogma to contain gene-set analyses. Version 3 of the database gathered information from more than 90 database resources based on a consolidated gene list. The system has continued to evolve; Version 5's Suite consists of the components described below, with regularly-supplied data and feature updates based on cycles comprising planning, implementation, development, semi-automated quality assurance, documentation (see https://www.genecards.org/Guide), and deployment. In parallel, new scientific enhancements are published in peer-reviewed journals, with the complete list of up-to-date publications provided at https://www.genecards.org/Guide/Publications.
Availability
GeneCards and many of the Suite members are free for academic non-profit institutions. Other usage requires a license from LifeMap Sciences (https://www.lifemapsc.com/contact-us/).
Additional GeneCards Suite Databases and Tools
MalaCards
MalaCards (https://www.malacards.org) is an integrated database of human maladies and their annotations, modeled on the architecture and richness of the popular GeneCards database of human genes.
GeneHancer
GeneHancer (PMID: 28605766) is a regulatory element database within the GeneCards® Suite, with 400,000 enhancer and promoter entries, covering 18% of the genome. Integrating key epigenetic resources, GeneHancer creates a unique non-redundant and comprehensive view of regulatory elements annotated with functional information including accurate genomic coordinates, target gene associations, transcription factor binding sites, and tissue specificity patterns. GeneHancer is widely used to annotate and interpret non-coding variants, and is included as a native regulation track at the UCSC genome browser.
GeneCaRNA
GeneCaRNA (https://www.genecards.org/genecarna) is a searchable, integrative database that provides comprehensive, user-friendly information on all non-coding RNA (ncRNA) human genes. GeneCaRNA inherits its capabilities from the GeneCards framework within which it is embedded. The GeneCards infrastructure encompasses >150 automatically-mined data sources; a large number of them contribute ncRNA annotations.
PathCards
PathCards (https://pathcards.genecards.org) is an integrated database of human biological pathways and their annotations. Human pathways were clustered into SuperPaths based on gene content similarity. Each PathCard provides information on one SuperPath which represents one or more human pathways.
GeneAnalytics (license required)
GeneAnalytics (https://geneanalytics.genecards.org), is a comprehensive and easy-to-apply gene set analysis tool for rapid contextualization of expression patterns and functional signatures embedded in the postgenomics Big Data domains, such as Next Generation Sequencing (NGS), RNAseq, and microarray experiments. GeneAnalytics’ differentiating features include in-depth evidence-based scoring algorithms, an intuitive user interface and proprietary unified data.
VarElect
VarElect (https://varelect.genecards.org/) is a cutting edge Variant Election application for disease/phenotype-dependent gene variant prioritization. It is an effective and user friendly tool for analyzing genes with variants following Next-Generation Sequencing (“NGS”) experiments. VarElect can rapidly prioritize genes that have been found to have variants according to selected disease/phenotype - gene associations. VarElect leverages the rich information within GeneCards®, the leading human gene database, MalaCards, the human disease database, LifeMap Discovery®, the regenerative medicine database, and PathCards, the unified human biological pathways database.
GenesLikeMe
GenesLikeMe (https://glm.genecards.org) is a novel analysis tool, which provides a similarity metric by highlighting shared descriptors between genes, based on the rich annotation within the GeneCards compendium of human genes. Users supply a query gene, and the system finds putative functional paralogs, namely genes that are similar to the query gene based on combinatorial similarity of attribute annotations.
GeneALaCart (license required)
GeneALaCart (https://genealacart.genecards.org) is a gene-set-orientated batch-querying engine based on the popular GeneCards database. It retrieves selected annotations information about multiple genes in a variety of formats.