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. 2015 Jan;43(Database issue):D36-42.
doi: 10.1093/nar/gku1055. Epub 2014 Oct 29.

Gene: a gene-centered information resource at NCBI

Garth R Brown  1 , Vichet Hem  1 , Kenneth S Katz  1 , Michael Ovetsky  1 , Craig Wallin  1 , Olga Ermolaeva  1 , Igor Tolstoy  1 , Tatiana Tatusova  1 , Kim D Pruitt  1 , Donna R Maglott  1 , Terence D Murphy  2
Affiliations

Gene: a gene-centered information resource at NCBI

Garth R Brown et al. Nucleic Acids Res. 2015 Jan.

Abstract

The National Center for Biotechnology Information's (NCBI) Gene database (www.ncbi.nlm.nih.gov/gene) integrates gene-specific information from multiple data sources. NCBI Reference Sequence (RefSeq) genomes for viruses, prokaryotes and eukaryotes are the primary foundation for Gene records in that they form the critical association between sequence and a tracked gene upon which additional functional and descriptive content is anchored. Additional content is integrated based on the genomic location and RefSeq transcript and protein sequence data. The content of a Gene record represents the integration of curation and automated processing from RefSeq, collaborating model organism databases, consortia such as Gene Ontology, and other databases within NCBI. Records in Gene are assigned unique, tracked integers as identifiers. The content (citations, nomenclature, genomic location, gene products and their attributes, phenotypes, sequences, interactions, 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 Entrez Direct) and for bulk transfer by FTP.

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Figures

Figure 1.
Figure 1.
Upper portion of Full Report display in Gene. The record for the human RBP4 gene is shown. The complete report is divided into collapsible sections listed in the Table of contents; only the Summary section is shown. Other report formats are available from the Display settings menu. The ‘Hide sidebar’ button removes the right hand Discovery column from the display. Complete documentation (http://www.ncbi.nlm.nih.gov/books/NBK3841/) is available by following the Help link.
Figure 2.
Figure 2.
Tabular format view. The Tabular format is the default display setting when a query of Gene returns more than one record. A subset of the 107 records returned from a query using the gene symbol RBP4 is shown. The Name/Gene ID column contains links to each Gene record. Results can be refined further in several ways, including by Organism, by any of the filters in the left column and by user-specified filters managed through MyNCBI. Search result sets can be downloaded using the ‘Send to:’ menu.
Figure 3.
Figure 3.
Genomic context section of the Full Report. The section for the human RBP4 gene is shown, with the sidebar collapsed. Information about the location of the gene on the current and previous annotation releases is provided in a table and includes links to NCBI's Assembly database. The graphic displays neighboring genes and their orientation, and each gene symbol links to the corresponding Gene record for easy navigation.
Figure 4.
Figure 4.
Genomic regions, transcripts and products section of the Full Report. The section for the human RBP4 gene is shown. This is an interactive display of the location of a gene annotated on a genomic RefSeq. More than one genomic RefSeq sequence may be available, and the gene's location on any can be displayed using the drop down menu at the top. Zoom and panning functions are enabled, and the tracks displayed can be configured using the ‘Configure’ button. By default, the Genes track displays a merged rendering of transcripts and coding regions. Complete documentation is available by clicking the ‘?’ icon.
See this image and copyright information in PMC

References

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