Entrez Gene: gene-centered information at NCBI

By Donna R. Maglott, James Ostell, Kim D. Pruitt, Tatiana A. Tatusova. Nucleic Acids Res., 2006

1,818 citations recorded by the source corpus.

Entrez Gene () is NCBI's database for gene-specific information. Entrez Gene includes records from 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 both curation and automated integration of data from NCBI's Reference Sequence project (RefSeq), from collaborating model organism databases and from other databases within NCBI. Records in Entrez Gene 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 provided via interactive browsing through NCBI's Entrez system, via NCBI's Entrez programing utilities (E-Utilities), and for bulk transfer by ftp.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/93c5caa9159ce66375723feed6b6023192f3c0f5

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Citations in the corpus

Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments (2013, background): “In the interest of clarity, most descriptions of TFs will be omitted, but may be found along with further references at RefSeq (28) and Entrez (29).”
Allen Brain Atlas: an integrated spatio-temporal portal for exploring the central nervous system (2012, methodology): “For ISH data and transcriptome data (microarray and RNA sequencing), gene expression data can be searched using specific gene symbols, gene names or Entrez Gene IDs (13).”
The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse (2013, background): “While these methods have led to identification of a great number of enhancers in the human and mouse genomes [3,25,29], the current computational techniques have thus far been limited by the small number of the training set samples and limited number of chromatin modifications examined.”
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists (2008, positive): “Most of the tools have likely adopted the existing work of another major group such as the NCBI Entrez Gene database (89).”
NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy (2011, background): “Gene (3), the Conserved Domain database [CDD (4)], dbSNP (5) and externally, including nomenclature groups, model organism databases, protein-focused resources and many more.”
Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation (2016, methodology): “Otherwise we revert to using Rfam (38), mirbase (39), UniProt or EntrezGene (40) names and, if there is no other option, a clone name.”
Gene: a gene-centered information resource at NCBI (2014, background): “The Gene database is a resource of the National Center for Biotechnology Information (NCBI) that centralizes generelated information into individual records (1).”
The UCSC Genome Browser (2003, neutral): “The RefSeq Genes track ( Maglott et al., 2011 ) ( Sayers et al., 2011 ), Ensembl Genes ( Flicek et al., 2011 ), GeneLynx ( Lenhard et al., 2001 ), GeneCards ( Safran et al., 2010 ), AceView, PubMed ( Sayers et al., 2011 ; UNIT 1.3), the HUGO Gene Nomenclature Committee Database (HGNC; Seal et al.,…”
NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins (2004, background): “Entrezqueries from the Entrez home page, where it is possible to query against all of the Entrez databases at once, will also return results to the Entrez Gene and Genomes (14) databases, which are both components of the RefSeq project.”
The Extracellular Matrix: Tools and Insights for the “Omics” Era (2015, methodology): “The protein-centric lists originally defined were then turned into gene-centric lists using NCBI Entrez Gene as reference gene database [27].”
Linking Human Diseases to Animal Models Using Ontology-Based Phenotype Annotation (2009, methodology): “Additional phenotype annotations were retrieved for crossspecies comparison from MGI [33], ZFIN [13], GAD [63], NCBI gene [64], and homologene [65] in September 2008.”
The Human Gene Mutation Database: 2008 update (2009, neutral): “complementary data sources are provided here (Genome Database (GDB) [4], Online Mendelian Inheritance in Man (OMIM) [5], HUGO Gene Nomenclature Committee (HGNC) [6], Entrez Gene [7], GeneCards [8], GenAtlas [9], GeneClinics [10], UniGene [11], SwissProt [12] and the Human Protein Reference Database ”
miRTarBase: a database curates experimentally validated microRNA–target interactions (2010, background): “Generally, web pages of the miRTarBase contain many effective quick links to several other web resources, including NCBI Entrez (21), UCSC Genome Browser (22), miRBase (2), BioGPS (23), iHOP (24) and HGNC (25).”
DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis (2007, methodology): “Some integrated databases, such as NCBI Entrez Gene [1], UniProt [2], PIR [3], etc., made great efforts to integrate annotation resources in one centralized location and are considered to be the world-class bioinformatics foundation for general bioinformatics purposes.”
PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors (2013, positive): “By integrating information from Entrez Gene (33), UniProtKB (34), GeneRIF (33) and mined by ourselves, we added related references for TFs. Evolutionary conserved elements may work as transcriptional regulatory elements (35,36).”
Genenames.org: the HGNC resources in 2015 (2014, background): “Orthology assertions can also be obtained for a gene by searching with its Ensembl gene identifier or its NCBI Gene identifier.”