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. 2011 Jan;39(Database issue):D52-7.
doi: 10.1093/nar/gkq1237. Epub 2010 Nov 28.

Entrez Gene: gene-centered information at NCBI

Donna Maglott  1 , Jim Ostell, Kim D Pruitt, Tatiana Tatusova
Affiliations

Entrez Gene: gene-centered information at NCBI

Donna Maglott et al. Nucleic Acids Res. 2011 Jan.

Abstract

Entrez Gene (http://www.ncbi.nlm.nih.gov/gene) is National Center for Biotechnology Information (NCBI)'s database for gene-specific information. Entrez Gene maintains records from genomes which have been completely sequenced, which have an active research community to submit gene-specific information, or which are scheduled for intense sequence analysis. The content represents the integration of curation and automated processing from NCBI's Reference Sequence project (RefSeq), collaborating model organism databases, consortia such as Gene Ontology and other databases within NCBI. Records in Entrez Gene are assigned unique, stable and tracked integers as identifiers. The content (nomenclature, genomic location, gene products and their attributes, markers, phenotypes and links to citations, sequences, variation details, maps, expression, homologs, protein domains and external databases) is available via interactive browsing through NCBI's Entrez system, via NCBI's Entrez programming utilities (E-Utilities) and for bulk transfer by FTP.

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Figures

Figure 1.
Figure 1.
Representative ‘Summary’ report of query results. Result (partial) of a query to retrieve information about gckr as a gene symbol in mammals or fungi. This figure illustrates several points: (i) use of field restriction in the query; (ii) the display when ‘Limits’ is invoked to restrict results, in this case by species; (iii) use of ‘Display Settings’ to report five records per page ordered by Gene Weight (computed by number of gene-specific citations and conservation) and (iv) use of MyNCBI to highlight matches to the query term in the result set in green. ‘Limits Activated’: Mammalia, Fungi indicates that Mammalia and Fungi were both checked on the form accessed from ‘Limits’ over the query bar. Of the 15 results that were returned, the information under ‘Filter your results’ at the upper right indicate that 11 are current (Current Only, highlighted), 5 have genotype information available in dbSNP (Gene Genotype), 9 can be viewed in Map Viewer (Gene Map Viewer) and 8 have expression data in UniGene (Gene UniGene). For each GeneID returned by the filtered query, the summary includes the species, preferred and alternate symbols, preferred and other descriptive names, chromosome localization, the GeneID and the MIM number when appropriate. Click on any symbol to link to the full report or click on the Entrez Gene text at the upper left to return to Entrez Gene’s home page. The ‘Find related data’ menu in the column at the right allows selecting a database in which to find data related to initial query results. For example, to look for homologs of genes in a result set, select HomoloGene from the menu, read about how these links are calculated and click on ‘Find items’.
Figure 2.
Figure 2.
Representative full report in Entrez Gene. This figure is based on http://www.ncbi.nlm.nih.gov/gene/7097 with several sections closed to allow the report to fit on one page. Note that the concepts enumerated in the Table of Contents at the upper right are provided explicitly in the Entrez Gene full report; concepts enumerated in the Links section are presented from other resources at NCBI. Some of the titles in the Links section do not correspond exactly to the name of an NCBI database. For example, RefSeq proteins result in a display in the Protein database; RefSeq RNA and RefSeqGene result in displays in the Nucleotide database and SNP GeneView results in the gene-specific display from dbSNP.
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