Entrez Gene Help: Integrated Access to Genes of Genomes in the Reference Sequence Collection

Summary

Figure 1

In the Summary format, each result is numbered, and a check box is provided at the left of the number. The check box enables you to select which of the records in the retrieval set that you want to review in another format, according to your selection in the Display menu. If none is checked, all are displayed in the selected format.

Figure 1C

• 1

  Official symbol

• 2

  Locus tag

• 3

  First symbol in the synonym list

Figure 2. Representation of Links in Entrez Gene. (more...)

Figure 2. Representation of Links in Entrez Gene. Links to additional information are provided in multiple formats and with different content. In the summary views (Summary, Brief), the word Links at the upper right of the page expands to a navigation menu to other NCBI databases (A). If you have configured your My NCBI environment to display the menu as plain text, the menu will be written out as in Figure 1. Within the Full Report and Gene Table display options, the menu also includes includes a summary of the links to non-NCBI resources mentioned in the record (B).

Figure 2A

The summary display allows you to reorder the results by several methods:

• Relevance (the current default). Relevance is calculated from Gene's assessment of what fields are the most important by which to find search results. For example, Gene assigns more value to results if they match a term in the 'Gene Name' (symbol) field than to a match in free text such as the RefSeq or GeneRIF summary. Thus if your query is the single term 'cat', then records with symbols of 'cat' will be sorted ahead of records with the term cat only elsewhere in the record.
  
  

• Gene Weight. Gene Weight is calculated from multiple lines of evidence geared toward evaluating how well a gene has been characterized. These lines include:
  
  

  • 1

    Informative Gene-PubMed links. Informativeness is inversely proportional to the number of Genes connected to a PubMed record.
    
    

  • 2

    Informative symbols or full names. A gene with a symbol constructed as LOC+GeneID is weighted less, for example, than a gene with the symbol 'ABCA1'. A gene with a description that starts with the word 'hypothetical' is weighted less than one with a description that starts with 'cystic fibrosis'.
    
    

  • 3

    Inclusion in HomoloGene or Protein Clusters. Genes (or their products) that are known to be conserved are weighted more highly.
    
    

  • 4

    Inclusion in OMIM or Books.
    

• Gene symbol
  
  

• Chromosome. Choosing this option causes the records to be sorted in this order:
  
  

  • 1

    Alphabetically by organism name
    
    

  • 2

    Numerically by chromosome
    
    

  • 3

    Numerically by the start position on the chromosome.
    
    For example, suppose that the search results include genes for Homo sapiens (human) and Mus musculus (mouse). The human genes will all appear before those for mouse. Within the set of human genes in the results, those that are placed on chromosome 1 will appear first, followed by those placed on chromosome 2, and so on. Finally, within a chromosome, genes will be sorted according to their start positions on the chromosome. Genes that are not placed on a chromosome will appear at the end of the results. Genes that are placed on multiple chromosomes will be sorted according to the first such chromosome.

Brief

The functions allowed from the Brief display are similar to those described from the Summary display. The purpose of the Brief option is to support a more compact result set while providing enough information (the preferred symbol, 20 characters of the full name, and the GeneID) for you to select records to display a Full Report.

Gene Table

The Gene Table display represents the gene structure as annotated on the current genomic RefSeq representing the reference genome. This annotation is updated only with each comprehensive re-annotation cycle at NCBI (a build), usually no more than twice a year. This means that if the version of a RefSeq RNA has changed, or if the number of transcript variants has changed, the table will be out of date with respect to the Reference Sequences section of the full Gene report.

The table reports the intron/exon organization of each transcript, and, if an mRNA, the region of each exon that contains coding sequence (sample). It does this in two ways:

• graphically, by repeating the display included in the Full Report

• in a table, by reporting the position of any exon, intron, or coding region

Table 2. Access to sequence information from the (more...)

Table 2. Access to sequence information from the Gene Table display option.

Scope	Link to use
Complete gene feature	Options from the menu opened by clicking on the genomic RefSeq accession (format NC_, NW_ NT_) at the top of the graphic display.
Complete RNA	Options from the menu opened by clicking on the RNA RefSeq accession (format NM_, NR_, XM_, XR_) at the left of the graphic display. Display in GenBank format from the RNA RefSeq accession at the top of the accession-specific subsection of the table.
Complete protein	Options from the menu opened by clicking on the Protein RefSeq accession (format NP_, XP_) at the left of the graphic display. Display in GenBank format from the protein RefSeq accession at the top of the accession-specific subsection of the table.
Single intron, exon, or coding sequence (CDS)	Display in FASTA format from the range shown in the corresponding table column.

Please note that this function is not supported when the gene has not (yet) been annotated on any of NCBI's Genomic RefSeqs.

The sequence being retrieved is from the indicated genomic sequence, not the RNA. This means that the length of a poly(A) tail is not included in the report.

When viewing the sequence-specific nucleotide or protein record, use the Display options to generate the format you prefer.

Because the Gene Table reflects the annotation on the current genomic sequence, for bulk access you may prefer to use the seq_gene.md.gz file in the species-specific mapview subdirectory. These files are available for genomes that can be viewed in Map Viewer. For example:

• Human

• Mouse

The data in Gene Table reflect the current NCBI batch annotation, so it is possible that the RefSeq mRNAs, which are updated continuously, have changed. Check also the Reference Sequences section of the Entrez Gene record to determine whether updates have occurred (new versions and/or more variants and/or suppression resulting from review).

Navigation: In the Genomic regions, transcripts, and products section, the mRNA and Protein links in the table are hyperlinked to the Exon information table specific to that accession.

To the right of the Exon information tables are blue-shaded icons:

• top of the page

• table for the previous product

• table for the next product

UI List

This display is essentially the same as that of the Brief format, with the addition of the unique identifiers (UIs) for a Gene record on the second line. The difference between the Brief and UI List displays is more apparent, however, when selecting the Send to Text option. For the UI List, only the Gene identifiers are reported.

Navigation Menu

Figure 2

Table of Contents lists the subcategories of information available for a gene. Clicking on the name of the subcategory takes you to that portion of the gene record. The arrow pointing up on the bar separating subcategories ( ) will return you to the top of the page, should you want to make a different selection from the menu.

Links contains standard links seen in all Entrez records, followed by links to sites of interest not in the Entrez system. The LinkOut option is always last in this section when available.

Entrez Gene Info enumerates resources that may help you find and understand the information in Gene. The Help link goes to the default help document. The default help document is also accessed by the question marks ( ) in the horizontal section separators.

Feedback enumerates several sites where you can comment on or add data to Gene and/or RefSeq.

Subscriptions provides links to forms where you can subscribe to a mailing list to receive announcements about updates to Gene, Map Viewer, and RefSeq.

Title

Figure 3. Representative title section of the (more...)

Figure 3. Representative title section of the Full Report display (A). This section provides the symbol and full name of the gene, the GeneID, and the last date any information in this record was changed (B). See Figures 4–8 for subsequent section views of the Full Report display.

Figure 3A

The second line of the title section contains the NCBI GeneID and the last date a record was changed. The date is in the format day-month-year. Change is defined as any modification to the content of the record, including ancillary changes such as the URL for a displayed link.

Summary

Figure 4. Representative Summary (A) and Genomic regions, (more...)

Figure 4. Representative Summary (A) and Genomic regions, transcripts, and products sections (B) of a Full Report display. Each accession in this display is hyperlinked to the Nucleotide or Protein databases as appropriate, where standard tools exist to facilitate downloading sequence.

Figure 4

Official Symbol: and Name: Nomenclature provided by the named external authority.

Identifier from the primary data provider: Identifier and link to the major resource outside of NCBI that provided information about this gene.

Locus tag for the record is in the next line. Locus tag corresponds to the systematic feature qualifier used by the international sequence collaboration (DDBJ/EMBL/GenBank) and can be assigned by sequence submitters as a unique, systematic gene descriptor. When such a value is not available from submitted sequence, the identifier from a collaborating model organism database is used. Locus tag is often used to anchor a link to a database other than Entrez Gene. Locus tag is also used as the preferred symbol if an official symbol has not been identified for a gene.

Gene type: Possible values are tRNA, rRNA, snRNA, scRNA, snoRNA, miscRNA, protein-coding, pseudo, other, and unknown. These are indexed as properties of a gene by using the terms:

• genetype trna (transfer RNA, tRNA)

• genetype rrna (ribosomal RNA, rRNA)

• genetype snrna (small nuclear RNA, snRNA)

• genetype scrna (small cytoplasmic RNA)

• genetype snorna (small nucleolar RNA)

• genetype miscrna (miscellaneous RNA)

• genetype protein coding

• genetype pseudo (pseudogene)

• genetype other (when the type is known, but there is no specific enumeration for it)

• genetype unknown (when the type of gene is uncertain)

RefSeq status: Any of the set of status descriptions defined by RefSeq.

Organism: The binomial, and strain when appropriate, with a link to the NCBI Taxonomy database.

Lineage: Binomial and lineage from the Taxonomy database.

Also known as: Unofficial symbols and descriptions that have been used for this gene and its products. If there is no official symbol, and no locus_tag, the symbol at the top of the display is repeated in this section. These names are integrated from several sources, including model organism databases, annotation on sequence records, and interactive curation from the published literature.

Table 5. Other properties.

Table 5. Other properties.

Property name	Explanation
alive	The record is current and primary (i.e., not secondary or discontinued). The term secondary is applied to any record that has been merged into another. This occurs most often when multiple genes are defined based on incomplete data, and these are later discovered to be parts of the same gene. One gene record then becomes secondary to the other.
GeneRIF	A record having one or more GeneRIF annotations attached.
has ccds	A gene that encodes a protein sequence that is a member of a Consensus CDS (CCDS). See http://www.ncbi.nlm.nih.gov/projects/CCDS/.
has RefSeqGene	This Gene record has an associated gene-specific genomic RefSeq in the RefSeqGene class.
has summary	A record with summary text (gene.summary)
has transcript variants	A record having two or more associated RefSeq transcripts, i.e., splice variants. Note: This is limited to RefSeq annotation and should not be used to identify all genes exhibiting alternative splicing, promoter usage, and/or polyadenylation signals.
hiv1interactions	Genes with curated HIV-1:human protein interaction data. See http://www.ncbi.nlm.nih.gov/RefSeq/HIVInteractions/index.html
Interaction	A record with data in the Interaction section.
officially named	A record with official nomenclature.
Phenotype	A record including a named phenotype.
Phenotype only	A record for a mapped phenotypic trait for which the molecular basis in not known.

Genomic Regions, Transcripts, and Products

Figure 4B

• view the intron/exon/coding region organization of a gene and its RNA product, or the placement of a pseudogene, on a genomic RefSeq

• identify the RefSeqs that correspond to any RNA or protein product and see an overview of the exons they represent

• navigate to the genomic, RNA, or protein sequence, by clicking on the RefSeq accession

• navigate to Blink, from the protein accession, to review how this protein sequence compares to related proteins from other taxa

For some species, including human and other vertebrates, the genomic RefSeqs are updated independently of the annotated product RNAs, with the latter being updated more frequently. This means that several kinds of discrepancies between the diagram and the current RefSeq RNAs may result.

• The diagram may be labeled with an mRNA accession (for a predicted transcript) of the format XM_123456, yet clicking on that accession results in an entry in Entrez Nucleotide that indicates that this accession is no longer primary. That means that a curated mRNA (accession of the format NM_123456 or NM_123456789) has been generated to replace the previous model accession. This new "NM" accession will be reported in the Reference Sequences section.

• The diagram may be labeled with curated RNA accession numbers (of the format NM_123456 or NM_123456789 or NR_123456) different from those listed in the RefSeq section. This will result if curation after the submission of the annotated genome identified more transcript variants, which therefore are listed only in the Reference Sequence section but not in the diagram. It will also result if curation after submission of the annotated genome identified an error in the annotated product, and the accession for that product was suppressed. In that case, the Genomic regions, transcripts and products section will indicate a transcript not listed in the RefSeq section of the Entrez Gene report.

Genomic Context

Figure 5A

If the gene has been included in a genomic annotation, the section also diagrams neighboring genes and indicates their orientations. If the name of a gene is too long to use for a label, truncation is indicated by an ellipsis (...). The gene being shown on the diagram is in maroon. All other diagrams and labels anchor links to specific gene pages, supporting quick navigation to review neighboring genes by clicking in the area of the symbol/arrow.

If a gene has not been included in the current version of the annotated genome provided in NCBI RefSeqs, the Genomic context section will not include a diagram but will report the map location. If the gene is annotated on more than one genomic RefSeq, only one will be used for the graphic display, but the location information will be provided in the ASN.1 of the record and in the Reference Sequences Section.

Bibliography

Figure 5B

Figure 5C

Interactions

There are two major subcategories of information reported as Interactions: HIV-1 interactions and general interactions.

Alleles

This section reports the general characteristics of alleles that have been described for a gene and provides links to more detailed information. This function is being phased in gradually; the current set is for mouse and is being developed from information supplied by Mouse Genome Informatics.

General Gene Information

This section includes several subcategories of information, including:

GeneOntology (GO): The specific GO terms are listed by source of the information, category, term, evidence information, and links to supporting publications. Each GO term supports a link to the AmiGO browser. Abbreviations in the Evidence column indicate the level of support for assigning a GO term to a gene. Explanations for these abbreviations are provided by the Gene Ontoloogy website.

Entrez Gene does not alter the associations provided by a model organism database, nor does Entrez Gene recapitulate the directed acyclic graph structure provided by GO. Thus, Entrez Gene does not support retrieval of all genes associated with a specific GO term based on that term's parent. If you identify a GO term that is inappropriate for a gene, please contact the model organism database directly. ftp://ncbi.nih.gov/gene/DATA/go_authorities.xml documents the authorities Entrez Gene uses to connect GO terms to GeneIDs.

Homology: A partial listing, with links, of orthologs in other species. Other views of homology data are available from TaxPlot and the HomoloGene link in the Links menu.

Phenotypes: A description of the effect of the gene on phenotype, especially disease. Links to more information are provided as available, as in the case of human disease and links to OMIM.

Figure 6. Representative General gene information (more...)

Figure 6. Representative General gene information section of a Full Report display. Note that the Markers subsection is provided in a scrolling window.

Figure 6

Pathways: A description of pathways that include this gene with links to more information about that pathway.

Relationships: This section reports some of the public sequences that were used support the prediction of the indicated RefSeq model. Thus this section is used only for those genomes for which NCBI calculates annotation, and only for those genes where there is not a supporting curated RefSeq. Sequence accessions reported in this section may differ from those for which alignments are displayed from Evidence Viewer for this gene.

General Protein Information

This section applies only to genes that encode proteins. It reports the name or names that have been assigned to proteins encoded by the gene and provides other descriptive text. The names are as annotated on the RefSeq protein, when that protein is available. The sources of these names include model organism databases, annotation on public sequence databases, and curation by RefSeq staff.

NCBI Reference Sequences (RefSeqs)

This section describes the gene-specific NCBI reference sequences (RefSeqs) that have been established for this gene. In addition to enumerating the accession numbers and providing links to the appropriate Entrez sequence database, this section may also include descriptions of each transcript variant, accession numbers of the public sequences used to support any transcript, and a listing of computed domains in an encoded protein. The text provided in this section therefore supports retrieving gene records based on descriptions of conserved domains.

The Reference Sequence group uses several approaches in maintaining information. These can be broadly categorized as:

• 1
  

  

  Figure 7. Representative NCBI Reference Sequences (more...)

  

  Figure 7. Representative NCBI Reference Sequences (RefSeq) section in the Full Report display. This section includes two subsections: RefSeqs maintained independently of Annotated Genomes (A), and RefSeqs of Annotated Genomes (see Figure 8). The RefSeqs maintained independently of Annotated Genomes includes: B, mRNA and Protein(s) accession numbers, a Description of the transcript, links to the Source sequence(s) from which the Reference Sequences are derived, and links to the Consensus CoDing Sequence database (Consensus CDS); and C, links to the Conserved Domains database.

  RefSeqs maintained independently of Annotated Genomes (Figure 7). RefSeq RNA and protein sequences are updated continuously, independently of any comprehensive reannotation of a genome. Because these reference sequences are curated independently of the genome annotation cycle, their versions may not match the RefSeq versions in the current genome build. You can identify updates by comparing versions in this section to versions in the Genomic regions, transcripts, and products section.

• 2
  

  

  Figure 8. Representative subsection RefSeqs of Annotated (more...)

  

  Figure 8. Representative subsection RefSeqs of Annotated Genomes (A) in the NCBI Reference Sequences (RefSeq) section of a Full Report display. This subsection follows RefSeqs maintained independently of Annotated Genomes (see Figure 7). It includes the accession numbers in the available Genomic assemblies, in this case the Reference assembly and the Alternative assembly from Celera with links to the GenBank and FASTA records (B). In this example, the gene is annotated on the complementary strand in all genomic accession numbers (C), and no model mRNA or protein accession numbers were created. Note that some RefSeqs for this gene have been suppressed and are listed under the Suppressed Reference Sequences subsection (D).

  RefSeqs of Annotated Genomes (Figure 8). This section reports genomic RefSeqs from all assemblies on which this gene is annotated, such as RefSeqs for chromosomes and scaffolds (contigs) from both reference and alternate assemblies. The position and strand of the gene feature is provided (offset 1) .GenBank and FASTA anchor links to sequence in the given formats. Model RNAs and proteins are also reported here.

• 3

  Genome Annotation. RefSeq RNA and protein sequence are provided only through the process of genome/chromosome annotation.

• 4

  Suppressed Reference Sequence(s). Accession numbers listed in this section were suppressed for the cited reason(s). Suppressed RefSeqs do not appear in BLAST databases, related sequence links, or BLAST links (BLink) but may still be retrieved by from the Nucleotide or Protein databases, and by clicking on the hyperlinked accession.version.

Related Sequences

This section has two subsections, one in which the nucleotide sequence is primary and one for protein sequences only (UniProt). It contains sequence accessions that are related to the gene and provides links to the appropriate sequence record in Entrez Nucleotide , Entrez Protein or UniProtKB. It is not intended to be a comprehensive list of all sequences related to any gene; such sequences can more explicitly be found by using BLAST to query sequence databases or by using pre-calculated reports of related sequences via Entrez Nucleotide, Entrez Protein, or BLink. The sequence accessions in this section are provided in a tab-delimited format in the gene2accession.gz file in the DATA directory of the Gene FTP site.

Depending on the genome of the gene being reported, the sequences included may or may not be restricted to the same subspecies or strain.

Gene purposely lists protein accession numbers on records being represented as not protein-coding. The intent is to make the connection between sequence annotation and Gene's current representation of the type of gene. Users with evidence indicating that the Gene record should be reviewed are encouraged to contact the RefSeq staff.

Accessions are reported as related sequences based on several criteria:

• mRNAs with unique best placement on a genome coinciding with an annotated Gene

• cDNA/cDNA sequence relatedness (calculated based on criteria of identity, length of overlap to known accessions, and coverage of the novel accession)

• submissions from model organism databases or nomenclature authorities

• identification of proteins with identical sequences

• curation by RefSeq staff

• annotated GeneIDs from the ORFeome Collaboration or Celera

Additional Links

This section provides a printable view of a subset of links to information both within and external to NCBI. Some of these links overlap those included in the Links menu. The intent of this section is to provide a printable report of, for example, MIM numbers, UniGene cluster numbers, and family-specific websites.

ASN.1

The ASN.1 display provides gene records structured according to the Entrezgene specification. An XML transformation of the ASN.1 is also available. Detailed information about the specification is provided in the Tips for Programmers section.

XML

Any record or selected set of records can be displayed in XML format. The XML is generated automatically from the ASN.1 record that is used to support the display, with the names of the tags defined by the ASN.1 specification. Detailed information about the specification is provided in the Tips for Programmers section.

Introduction to Limits

Figure 9. Representative Limits Page. Shown is an (more...)

Figure 9. Representative Limits Page. Shown is an example of a Limits page used to find current records in Entrez Gene for Drosophila melanogaster that are associated with reviewed RefSeqs, are not pseudogenes, and have alcohol in the gene name. (A) Enter alcohol in the query box. (B) Set the filed name to Gene/Protein name. (C) See Exclude and check Pseudogenes. (D) See Include Only and check Current Records and RefSeqs. (E) See Limit by RefSeq Status and check Reviewed. (F) In Limit by Taxonomy, check Drosophila melanogaster in the Invertebrates subsection.

Figure 9A

Limits is designed to make it easier to execute certain queries by checking boxes, rather than by writing out the text of an Entrez query. It is particularly useful if you want to retrieve genes only:

• with a value found in a single known field (Figure 9B)

• from a particular cellular source or RefSeq representation (Exclude/Include only, Figure 9C)

• represented by a particular type of RefSeq (Limit by RefSeq Status, Figure 9D)

• from a taxonomic group (Limit by Taxonomy, Figure 9E)

Remember that once you have set Limits, that setting remains through multiple queries, unless you remove the setting. A yellow banner appears below the Limits tab when Limits is turned on. Turn off Limits at any time by removing the check to the left of the word Limits in the query bar of the result page.

Figure 9C

Figure 9C

• Genomic: Genes encoded by chromosomes or the major genomic macromolecule for the taxon.

• Mitochondria: Genes encoded by mitochondria.

• Plasmids: Genes encoded by plasmids.

• Plastids: Genes encoded by plastids.

• RefSeqs: Genes for which RefSeqs exist.

• NEWENTRY: GeneIDs used to support submission of GeneRIFs, by species, for a gene not currently in Entrez Gene.

Additional limits are:

• Limit by RefSeq Status (Figure 9D): To retrieve genes based on the type of RefSeq used to represent the gene.

• Limit by Taxonomy (Figure 9E): Make it easier to restrict your query by organism.

The additional limits are treated as Include Only and are hierarchical. For example, to limit your results to genes in invertebrate genomes, check Invertebrates. These selections are also treated as the Boolean operator OR, so if you want to retrieve genes from either Danio rerio or Xenopus sp., check both Danio rerio and Xenopus.

Table 4. Filter sets.

Table 4. Filter sets.

Filter name	Definition
all	Total records, current or not
gene all	All current records
gene books	Gene records with explicit links to Entrez Books
gene gensat	Gene records with explicit links to Entrez GenSAT
gene geo	Gene records with explicit links to Entrez GEO
gene homologene	Gene records with explicit links to Entrez HomoloGene
gene nucleotide	Gene records with explicit links to Entrez Nucleotide, excluding RefSeq chromosome or contig accessions
gene nucleotide pos	Gene records with explicit links to Entrez Nucleotide, limited to those of RefSeq chromosome or contig accessions, and thus including position data
gene omim	Gene records with explicit links to Entrez OMIM, and thus includes links to both disease and “gene” records in OMIM
gene protein	Gene records with explicit links to Entrez Protein, and thus includes links to GenPept and SwissProt accessions
gene pubmed	Gene records with explicit links to Entrez PubMed
gene snp	Gene records with explicit links to Entrez dbSNP, and thus supports finding gene variation information available in dbSNP
gene taxonomy	Gene records with explicit links to Entrez Taxonomy
gene unigene	Gene records with explicit links to Entrez UniGene
gene unists	Gene records with explicit links to Entrez UniSTS (marker data)

The Limits page also allows you to restrict queries by date. The options are:

• Creation Date (Figure 9F): Retrieve records created within the range entered, or according to pre-selected ranges in the pull-down menu.

• Last Modification (Figure 9G): Retrieve records modified within the range entered, or according to preselected ranges in the pull-down menu.

Examples Using Limits

A. To retrieve non-mitochondrially encoded NADH dehydrogenases from human, mouse, or rat, use the Limits form to:

• 1

  Enter nadh dehydrogenase in the query box (case does not matter).

• 2

  Select Gene/Protein name from the All fields drop-down menu.

• 3

  Check Mitochondrion under Exclude.

• 4

  Check Homo sapiens, Mus musculus, Rattus norvegicus.

• 5

  Press Go in the search bar.

B. To retrieve E. coli genes related to tryptophan, use the Limits form to:

• 1

  Check Escherichia coli.

• 2

  Enter tryptophan in the query box.

• 3

  Press Go in the search bar.

Table 3. Fields, filters, and properties in Entrez (more...)

Table 3. Fields, filters, and properties in Entrez Gene.

Field name	Definition [including field abbreviations]	Examples
Name subcategory
Disease name or phenotype of mutants	Disease or phenotype associated with the record. [DIS]	Find the genes that contribute to SCID. SCID[dis]
Gene name	A symbol for the gene. Includes preferred symbols, aliases, and locus tags. [SYM][SYMB][GN][GENE NAME]	Genes with a symbol starting with smt. smt*[sym]
Preferred symbol	The preferred symbol for the gene, not including aliases or locus tags. [PREF]	Genes with a preferred symbol starting with smt. smt*[pref]
Gene full name	Only the full name of the gene. [GFN][GENEFULLNAME]	Find genes with a full gene name of tumor protein p53: tumor protein p53[gene full name]
Gene/protein name	The short or full name of the gene or any of its protein products (when applicable). [TITL][TITLE][TF][TI][Protein]	Find genes that have the word kinase in GO annotation but do not have the word kinase in the name. kinase[gene ontology] NOT kinase[gene/protein name]
Protein full name	Only the full name of the protein products. [PFN][PROTEINFULLNAME]	Find genes with a full protein name of glutathione S-transferase M1: glutathione S-transferase M1[protein full name]
Location subcategory
Base position	Base position, relative to the genomic accession. This is supported only for the reference assembly and only for genomes where chromosome coordinates are defined. In general, the query should define a range of at least 100 kb; the range must be specified as a pair of integers. The query results will include genes that lie either partly or completely within the range specified. A query by base position should also specify the chromosome and organism. This can be done by including the chromosome accession, or alternatively, by including the chromosome and either the Taxonomy ID or the Organism.[CHRPOS,CPOS,CPOSITION]	NC_000012[nucl_accn] AND 9100000:9200000[chrpos] 9606[taxid] AND 12[chromosome] AND 9100000:9200000[chrpos]
Chromosome	Chromosome location of the gene. The value used is according to the convention of the source genome. In other words, if III is used, III but not 3 will be indexed in this field. [CHRM][CHR][CHROMOSOME]	Retrieve records containing the word kinase, and the gene is located on chromosome III:kinase AND III[chr] Retrieve records containing the words zinc and finger that are of human origin but not on chromosome 19: zinc finger NOT 19[chr] AND "Homo sapiens"[orgn]
Default map location	A map location in the units standard for the genome. For example, for human it is the cytogenetic band, for mouse it is the MGI map (centiMorgans). This is processed as a text field, so range queries are not implemented. For range queries, use Map Viewer. [MV][MVMAP]	Rat genes mapped to 18 q: rat[orgn] AND 18q[default map location]
Sequence subcategory In Gene: This means searching by sequence identifier, not by the sequence itself, which is managed by BLAST.
Nucleotide accession	An accession for a nucleotide sequence.[NACC]	There are instances where the same accession is applied to both nucleotide and protein sequences. To restrict an accession to nucleotide, use this field. (Accession numbers beginning with BC are not in this category.) BC052629[NACC]
Nucleotide UID	The gi of a nucleotide sequence.[NUID][NUCL_UID][NUCLEOTIDE_UID]	Many integer identifiers have overlapping number spaces. To find the gene record that corresponds to a given nucleotide gi from gene, use this field. 27363473[NUID]
Protein accession	An accession for a protein sequence. [PACC][PROT_ACCN]	There are instances where the same accession is applied to both nucleotide and protein sequences. To restrict an accession to protein, use this field. (Accession numbers beginning with three letters are not in this category.) AAH52629[PACC]
Protein UID	Protein gi. [PUID][PROT_UID][PROTEIN UID]	Many integer identifiers have overlapping number spaces, So to find the gene record that corresponds to a given protein gi from gene, use this field. 27363473[PUID]
Nucleotide or Protein accession	A sequence accession of any type. [ACCN]	Find all the genes encoded in accession AE003828: AE003828
Miscellaneous subcategory (alphabetical)
Creation date	Date the record was created. [cd][cdat][creation date]	Records containing the word xenopus created between February 5, 2004 and February 12, 2004: 2004/2/5:2004/2/12[cd] AND xenopus[orgn]
Date Discontinued	The date on which the record was discontinued[DIS_DATE][DDAT][DISCONTINUED][DISDATE]	Records discontinued between January 1, 2006 and December 31, 2006: 2006/1/1:2006/12/31[disdate]
Domain Name	Conserved domain and protein family names.[DOMAINNAME][DOM]	Retrieve records associated with the A2M family:A2M[domainname]
EC/RN number	Enzyme commission identifier for a product of the gene. Indexed without the EC prefix. [ECNO][EC]	Retrieve records where proteins have an E.C. number of 1.9.3.1: 1.9.3.1[ECNO]
Exon count	The number of distinct, non-overlapping RefSeq exons annotated for all RNA products of this gene interval, based on annotation in this priority: reference assembly first, alternate assembly second.This field can be queried by either a single integer value or a range.[XC][NUMEXONS]	Retrieve human records with one exon:human[orgn] AND 1[exoncount]Retrieve all records with a range of exons:10:20[exoncount]
Filter	Find records with a relationship to other data in Gene. For more examples of use of filters, see the Preview/Index section.	Retrieve records of mouse kinase genes with expression data stored in GEO: mouse[orgn] AND gene_geo[filter] AND kinase
Gene ID	Gene identifier. This field can be queried by either a single integer value or a range. [UID][ID][GeneID]	Many integer identifiers have overlapping number spaces. To find the gene record that corresponds to the human BRCA1 gene by GeneID, use this field: 672[GeneID]
Gene length	Gene length based on annotation in this priority: reference assembly first, alternate assembly second. If there are multiple placements, only on non-reference assemblies, then the longest value on non-reference assemblies is used.This field can be queried by either a single integer value or a range.[GL][GENELEN]	Retrieve all records with a gene span less than or equal to 5kb:1:5000[genelength]
Gene Ontology	GO terms applied to this gene AND the GO identifer as the integer. The terms include the component, function, and process categories.[GO][GENE ONTOLOGY]	Rat genes with GO terms starting with “kinase signaling” kinase signaling*[gene ontology] rat[orgn] Any gene with the GO id of GO:0004872: 4872[GO]
Group	Query terms to retrieve a set of genes with a specified relationship to another gene	Pseudogenes related to the same functional gene with GeneID = 11727 "related functional gene 11727"[Group]
MIM	Identifier assigned to human genes and phenotypes by OMIM [MIM]	Retrieve records that contain the MIM number 181510: 181510[MIM]
Modification date	Last date the record was modified.[MODDATE][MDAT][LMOD][DATE][UPDATED][MD]	Retrieve records for genes from eubacterial genomes last modified after March 10, 2004: eubacteria[orgn] AND 2004/3/10:2010/1/1[md] Retrieve records from sea urchins modified in the last 30 days: echinoidea[orgn]+AND+"last 30 days"[mdat]
Organism	Scientific and common names of organism[ORGN]	Find all records in Entrez Gene for the pig: pig[organism]
Property	An attribute of a Gene record based on its content.[prop][property]	Mouse records with transcript variants: mouse[orgn] AND "has transcript variants"[property]
PubMed UID	PubMed id. [PMID]	Many integer identifiers have overlapping number spaces. To find the gene record(s) that corresponds to a paper in PubMed from Gene, use this field: 12477932[PMID]
Taxonomy ID	Identifier for the species or strain in the NCBI taxonomy database. HINT: txid{value} also works, e.g., txid9606.[TAXID][TID]	Find all records in Entrez Gene for the pig: 9823[taxid] Alternatively: txid9823
Text Word	Any word in the record.[TEXT][WORD][AB][TXT]	Retrieve records that contain “32” in a record that also contains threonine, serine, and kinase: serine AND threonine AND kinase AND 32[TEXT]
UniGene cluster number	UniGene cluster including the text prefix. [UNIGENE][UGEN]	Hs.2[UNIGENE]

Filter

The term filter is used to describe categories of records that are grouped according to their relationship either to other Entrez databases or to external resources that have submitted LinkOut connections. If the former, the filter is named according to the pattern “gene other_Entrez_database”, such as “gene protein”. If the latter, the first two letters of the filter's name are ”lo”, for LinkOut. For a comprehensive listing of filters valid for the Gene database and the number of records in each, follow these steps:

• 1

  Click on the Preview/Index tab under the query bar.

• 2

  Use the pull-down menu named All Fields and select Filter.

• 3

  Click on the Index button to the right of Preview to see the filter names and the number of instances of each.

Properties

Properties are assigned to gene records based on content, rather than relationship to other database records, which is the role of filters (see Filter). At present, the properties assigned to Gene records fall into these major categories:

• Type of gene: Property named as genetype name_of_type.

• Source of the gene: Property named as source name_of_source.

• Type of RefSeq provided for the gene: Property named as srcdb refseq type_of_refseq.

• Other

The genetype option should be self-explanatory, except perhaps for miscrna, other, and unknown. Names for the types of molecules encoded by genes follow the conventions of the collaborating sequence databases (DDBJ/EMBL/GenBank); thus miscrna (misc_rna, miscellaneous RNA) is assigned to any gene that encodes an RNA product not included in the other specifics. The genetype other property is applied to loci of known type, but a specific category has not yet been applied in the Entrezgene data model (i.e., named fragile sites). The genetype unknown property is applied to probable genes for which the type is still under review. This category is frequently used when the defining sequence has uncertain coding propensity. Note: At the time of this writing, the assignment of gene records to the latter two categories continues to be refined. We appreciate your suggestions for any improvements.

The source options should be self-explanatory, with source other being used where a specific category has not yet been applied in the Entrezgene data model.

The srcdb refseq categories are as enumerated by RefSeq and will not be duplicated here.

Text Phrases

A text phrase is a special type of text search that uses two or more words to form a phrase. An ordinary text search of two or more words will find gene records that contain all of the specified words anywhere in the gene record. By contrast, a text phrase search will find gene records that contain all of the specified words together and in the specified order.

Table 6. Text phrases.

Table 6. Text phrases.

Text phrase	Explanation
“Annotation Information”	For genomes that NCBI annotates, Entrez Gene will represent information about the annotation of each current GeneID.  Text phrases will be attached to the gene data if the gene is not annotated well, or if annotation has changed in a complex way. Text phrases will also attached if there is no defining cDNA or genomic sequence for the gene, or if the GeneID was created after the most recent genome annotation. The goal is to facilitate retrieval of Gene records where the annotation on the RefSeq genomic records, if it exists, should be interpreted with caution. Thus records that are not known to have annotation issues can be retrieved by the query: NOT “Annotation Information” [Text] Specific sub-categories of annotation information are described below.
Sub-categories of annotation information
“partial on reference assembly“	The annotated gene, as suggested by the defining cDNA, is not complete.
“spans an assembly gap”	There is a gap in the assembly where the defining cDNA should align.
“suggests misassembly”	There are order/orientation issues suggested by the cDNA alignment.
“not annotated on reference assembly”	This gene is not annotated on the reference assembly.

Please note that the double quotes are included in the text phrases shown here because they are mandatory when performing a text phrase search.

DATA

DATA contains files that provide key attributes of genes, including:

• all associated accession numbers, including RefSeqs (gene2accession.gz)

• associated RefSeq accession numbers (gene2refseq.gz)

• citations (gene2pubmed.gz)

• nomenclature, ID, and map data (gene_info.gz)

• MIM numbers (mim2gene)

• UniGene clusters (gene2unigene)

• GO terms (gene2go)

Details of the construction of these files are reported in the (README) file.

DATA also contains the ASN_BINARY subdirectory. This path contains both a comprehensive extraction from Gene (All_Data.gz), several subsets categorized by source (Organelles, Plasmids), and subdirectories grouped broadly by taxonomy. Records of genes from species that are requested frequently are also provided in species-specific files, for example these mammals. The format of these extractions is compressed binary ASN.1. The program gene2xml is available to convert these files to XML or ASN.1 text.

The GENE_INFO subdirectory of DATA provides subsets of the gene_info file grouped broadly by taxonomy. This directory structure mirrors that of the ASN_BINARY path. Thus if you want the type of information provided in gene_info, but do not want to have to process the complete text, you can use one of the files in the appropriate subdirectory, for example these plants.

GeneRIF

GeneRIF contains files that provide supplemental information about gene functions, either from the GeneRIF pipeline (generifs_basic.gz) or the HIV-1, Human Protein Interaction Database (hiv_interactions.gz). The tab-delimited files are not subdivided by species of interest. All files except the file reporting GeneID/PubMedID relationships (gene2pubmed.gz) have a column with the ID from the NCBI Taxonomy database to facilitate the extraction of a subset of the data from the file by species.

Tools

Gene_tools provides or points to programs and scripts to mine data from Entrez Gene. Of particular interest is gene2xml, which can be used to convert the binary ASN.1 in the ASN_BINARY directory to XML or to ASN.1 in text format (README).