Entrez Gene: gene-centered information at NCBI

By Donna R. Maglott, James Ostell, Kim D. Pruitt, T. Tatusova. Nucleic Acids Res., 2004

383 citations recorded by the source corpus.

Entrez Gene (www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene) is NCBI's database for gene-specific information. It does not include all known or predicted genes; instead Entrez Gene focuses on the genomes that have been completely sequenced, that have an active research community to contribute gene-specific information, or that are scheduled for intense sequence analysis. The content of Entrez Gene represents the result of curation and automated integration of data from NCBI's Reference Sequence project (RefSeq), from collaborating model organism databases, and from many other databases available from NCBI. Records are assigned unique, stable and tracked integers as identifiers. The content (nomenclature, map location, gene products and their attributes, markers, phenotypes, and links to citations, sequences, variation details, maps, expression, homologs, protein domains and external databases) is updated as new information becomes available. Entrez Gene is a step forward from NCBI's LocusLink, with both a major increase in taxonomic scope and improved access through the many tools associated with NCBI Entrez.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/9e011397a9d6e5ba6c68bb8b996480cab9ee337f

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Citations in the corpus

BioVenn – a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams (2008, methodology): “BioVenn currently supports cross-references to Affymetrix [8], COG [9], Ensembl [10], EntrezGene [ 11 ], Gene Ontology [12], InterPro [13], IPI [14], KEGG Pathway [15], KOG [16], PhyloPat [17] and RefSeq [18].”
GENECODIS: a web-based tool for finding significant concurrent annotations in gene lists (2007, methodology): “It uses the Entrez Gene database [8] as the backbone data structure to link the functional annotations imported”
Database resources of the National Center for Biotechnology Information: update (2004, background): “Entrez Gene. Entrez Gene ( 16 ), provides an interface to curated sequences and descriptive information about genes with links to NCBI’s Map Viewer, Evidence Viewer (EV), Model Maker (MM), BLAST Link (BLink), protein domains from the Conserved Domain Database (CDD) and other generelated resources.”
Metascape provides a biologist-oriented resource for the analysis of systems-level datasets (2019, background): “For example, the accidental deletion of records for a certain model organism in NCBI 38 may go undetected.”
ErmineJ: Tool for functional analysis of gene expression data sets (2005, methodology): “We maintain on the order of 30 different mouse, human and rat array annotation files for different platforms, as well as generic files for RefSeq [ 12 ] genes that can be used to construct annotation files for other platforms (available from our web site [13]).”
Systematic integration of biomedical knowledge prioritizes drugs for repurposing (2017, methodology): “DOAF mines Entrez Gene GeneRIFs (textual annotations of gene function) for disease mentions ( Xu et al., 2012 ).”
MeInfoText: associated gene methylation and cancer information from text mining (2008, methodology): “The general human gene information, including official gene symbol, aliases, description and function was retrieved from NCBI Entrez Gene [20].”