Entrez Gene: gene-centered information at NCBI

Abstract

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.

Figure 1

Summary view of query results. The query is collagen ix “alpha 2”. The phrase alpha 2 is submitted in double quotes to restrict the query for alpha followed by 2. Note that the box ‘current records only’ (A) is checked automatically; to retrieve outdated records, this box must be unchecked. The default Summary display option allows gene-specific links to many other resources both within NCBI's Entrez system and not (LinkOut, MGC cDNA clone) via the Links menu (shown expanded, B). The summary includes the species of origin, preferred and alternate (Other aliases) symbols, preferred and other (Other designations) descriptive names, chromosome localization, the GeneID. Click on any symbol to the left of the check box (C) to link to the full report (Figure 2). The top black navigation bar and the blue sidebar at the left provide general links to other sites, including Genome-specific resource guides (Genomic Biology), the FTP site, forms to submit feedback (Feedback), and forms to subscribe to mail lists to be informed of changes (Subscriptions).

Figure 2

Partial report page. The standard gene-specific report page starts with the preferred symbol (name) and description of the gene, the species and the ID. As appropriate, it provides links to key external resource, using the label ‘Locus tag’ consistent with feature annotation of a GenBank record. If the gene has been annotated on a RefSeq genomic sequence (NT_004511), a graphic is provided showing the placement of the gene and those of its neighbors. The accessions assigned to the mRNA and proteins are shown at the left and right respectively (NM_001852, NP_001843 in this case). Clicking on any of these accessions opens a menu of options to obtain the sequence. The menu attached to the protein accession (A) shows that you can link to the sequence in either FASTA, GenBank or graphical format, or use BLink (1) to display information about related proteins, or conserved domains. The Links menu at the upper right corner of the complete record (expanded in B) indicates what resources have information related specifically to this gene. Some of these links are the same as those seen on the summary display (Figure 1), but there are often additional Links to information not accessible directly from Entrez.