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

Introduction

With the increasing sequencing and annotation of key genomes, having a gene-based view of the resultant information is useful. Entrez Gene has therefore been implemented to supply key connections in the nexus of map, sequence, expression, structure, function, citation, and homology data. Unique identifiers are assigned to genes with defining sequences, genes with known map positions, and genes inferred from phenotypic information. These gene identifiers are tracked, and information is added when available. Entrez Gene can be considered as the successor to LocusLink, with the major differences being in greater scope (more of the genomes represented by NCBI Reference Sequences or RefSeqs) and in being integrated for indexing and query in NCBI's Entrez system.

To help you use Entrez Gene effectively, this document is divided into the following sections:

1. Maintaining the Data
2. Interpreting the Display
3. Query Tips with Examples
4. Tips for the Programmer
5. Connecting users of Entrez Gene to your web site (LinkOut)

Previous users of LocusLink may find the subsections Tips for Previous LocusLink Users helpful.

Maintaining the Data

New Records

Records are added to Gene if any of the following conditions are met:

• A RefSeq is created for a completely sequenced genome and that record contains annotated genes. In the case of RNA viruses with polyprotein precursors, annotated proteins are treated as equivalent to a 'gene'.
• A recognized genome-specific database provides information about genes (preferably with defining sequence) or mapped phenotypes.
• The NCBI Genome Annotation Pipeline reports model genes.

Gene records are not created for genomes incompletely represented by whole genome shotgun (WGS) assemblies, which are provided in terms of RefSeqs by the accessions of the pattern NZ_ABCD12345678.

The minimum set of data necessary for a gene record, therefore, is a unique identifier or GeneID assigned by NCBI, a preferred symbol, and any sequence information, map information, or official nomenclature from an authority list.

You may construct a URL to identify records created within a certain number of days before the current date by using the following:

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi? filters=on&orig_db=gene&cmd=search&DB=gene&term=[your query]&pmfilter_CDatLimit=[number of days]

such as the following, to find human records created within the last 31 days:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi? filters=on&orig_db=gene&cmd=search&DB=gene&term=human[organism]&pmfilter_CDatLimit=31

Updated Records

Existing records are updated when new information is received. For some genomes, this may occur when a genome is reannotated and corresponding RefSeqs are updated. For other genomes, this may occur when any information attached to a gene record is altered. At present, updates are processed twice weekly, with refreshed data appearing Tuesdays and Thursdays.

GeneRIFs, although displayed as part of a Gene record, are processed independently of the Gene record itself. Most GeneRIFs were provided by the staff of the National Library of Medicine's Index Section, and are integrated weekly. Those are available with the first update to Gene within a week.

The modification date, therefore, will be the later of any update to Gene or the GeneRIF supplement.

You may construct a URL to identify records updated within a certain number of days before the current date by using the following:

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi? filters=on&orig_db=gene&cmd=search&DB=gene&term=escherichia coli[organims]&pmfilter_MDatLimit=[number of days]

such as, to find records for Escherichia coli modified in the last 31 days:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi? filters=on&orig_db=gene&cmd=search&DB=gene&term=escherichia coli[organism]&pmfilter_MDatLimit=31

Suppressed Records

All previous records will be searchable in Gene by the GeneID only. If it is known that the suppressed record has been replaced with another, the URL to the current record is provided. This is of particular benefit to those interested in retrieving information about NCBI Gene predictions that have not been retained.

Tips for Previous Users of LocusLink

Display of all discontinued records, replaced or not, is an added function compared to LocusLink. In LocusLink, only replaced records, and a subset of discontinued records, could be retrieved.

Interpreting the Display

This section is divided according to the Display options provided by Entrez:

• Summary
• Brief
• ASN.1
• XML
• Full Report (Graphics, default)
• Gene Table
• UI List
• LinkOut
• Book Links
• Geo Links
• Nucleotide Links
• OMIM Links
• Protein Links
• PubMed Links
• SNP Links
• Taxonomy Links
• UniGene Links
• UniSTS Links

Summary Display

When you process a query, the result is displayed in the Summary format. You can see this by noting the word Summary in the Display box.

The summary display (Figure 1) provides a check box for selecting records to display, the preferred symbol, the complete full name if available, the binomial for the species (in square brackets), genomic location, and the GeneID. If the gene is on a named plasmid, then the plasmid name will be given as the location. The Links, provided at the right, support ready display of related records in Entrez, as documented in Table 1. To navigate to more information about specific records, check the records to display (the default being all) and select the display option in the gray query bar.

Figure 1. Sample Summary Display.

A summary display (Note display option set to Summary.) for the query homeo box homolog. When available, Gene uses the title for a gene supplied by the appropriate nomenclature committee. In this example, note that some nomenclature committees include, as part of their official name, information about the species that was used to define the name of the homolog. That part of the title is usually given in parentheses, and should not be confused with the binomial for the source genome, which is italicized and in square brackets.

Tips for Previous Users of LocusLink
The summary display format corresponds most closely to what was termed the Brief Display option in LocusLink, with the LocusID, symbol, species, full description, location, and array of colored boxes indicating available links. In Gene, there is no link from the location information to Map Viewer; that is provided in the Links menu instead. The array of colored boxes is also replaced by the Links menu.

The Summary Display option of LocusLink, which reported all alternate symbols and sequence accessions associated with a gene record, is not currently provided from Gene.

Brief Display

The functions allowed from the brief display are similar to those described from the summary display described in the previous section. This 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) to allow you to select records to display in full. The Links provided at the right of the display support ready display of related records in Entrez, including: Nucleotide sequences, Protein sequences, Books, GEO, HomoloGene, OMIM, SNP, UniGene, UniSTS, and Taxonomy. To see more information, check the records to display (the default being all), and select the display option in the grey query bar.

Tips for Previous Users of LocusLink

There is no exact precedent in LocusLink. The links in the Links menu at the right correspond to the color-coded links in LocusLink (Table 1), but there are many more in Entrez Gene than LocusLink supplied.

Table 1. Correspondence between LocusLink letters and Entrez Links
Letter in LocusLink	Link name	Scope
P	PubMed	All citations, including those established via GeneRIFs.
O	OMIM	The OMIM records based on the gene or the phenotype (human only).
R		Not implemented separately; included in Nucleotide.
G	Nucleotide	A subset of nucleotide links. ESTs are excluded unless the gene is defined by an EST; unannotated high throughput genomic (HTG) sequences are also excluded unless used as a source for a RefSeq.
P	Protein	A subset of protein sequences encoded by the gene.
H	HomoloGene	HomoloGene links based on shared GeneID.
U	UniGene	UniGene links based on shared nucleotide sequences.
V	SNP	Links to dbSNP for all variations related to the GeneID, variant by variant.
	GeneView in dbSNP	A display of all variations related to the GeneID, by placement in the gene. This is the view directly corresponding to the V link.
Note: Gene supports many more links from the menu at the right of the Summary and Brief views than than the color-coded letter icons LocusLink provided. For Gene, all that is required is a connection between Gene and another Entrez database. Thus there may be links to Books, GEO, UniSTS, Taxonomy, etc.

Full Report (default)

The Full Report includes diagrams and text to represent some of what is known about a gene. Access to additional information maintained in other resources within NCBI or external to NCBI is provided by the Links menu at the top right and by other HTML anchors within the page.

This section of the Help document is divided into the following subsections:

• Title
• Navigation menu
• Summary
• Genomic regions, transcripts and products
• Genomic Context
• Bibliography
• Interactions
• Alleles
• General Gene Information
• General Protein Information
• NCBI Reference Sequences (RefSeqs)
• Related Sequences
• Additional Links

If multiple records are selected for display, the start of each record is indicated by the numbered open box at the left and by the Links menu at the right.

Title

The first line of this section provides the preferred symbol and descriptive name in bold font, followed by the italicized binomial in square brackets. If there is a recognized authority for the gene nomenclature of a species, that is the source for these values.

The NCBI GeneID and the Locus tag for the record are 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.

The second line also includes the last date a record was changed 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.

Navigation Menu

The menu at the right of the Entrez Gene report supports navigation to multiple sites of interest. In some display formats, the menu can be expanded and compressed by clicking on the + or -, respectively. More details about each submenu follow.

Summary

The next section includes several categories of information for each gene as available. These include:

1. Nomenclature
Symbols and names provided by the named external authority.
2. 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 via the terms:
   • genetype trna
   • genetype rrna
   • genetype snrna
   • genetype scrna
   • genetype snorna
   • genetype miscrna
   • genetype protein coding
   • genetype pseudo
   • genetype other
   • genetype unknown

   More details about Gene Types are in the related subsection describing what is indexed by Gene as a property.

3. Gene or RNA name. The name assigned to the gene or its primary RNA product.
4. RefSeq status. Any of the set of status descriptions defined by RefSeq.
5. Organism. The binomial, and strain when appropriate, with a link to the NCBI Taxonomy database.
6. Lineage. Binomial and lineage from the Taxonomy database.
7. Gene Aliases. Unofficial symbols and descriptions that have been used for this gene and its products. If there is no official symbol, the symbol at the top of the display is repeated in this section.
8. Summary. Descriptive text about the gene, its cellular localization, its function, and its effect on phenotype.

Genomic regions, transcripts and products

This section is provided when a gene has been annotated on a genomic RefSeq, in other words when the position of a pseudogene, or the intron/exon/coding region information, is available in some genomic coordinate system. You can use this section to:

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

Each position of a gene product, when represented by a RefSeq RNA (accession NM_000000 or XM_000000 for mRNA, NR_000000 or XR_000000 for non-protein coding RNAs) and/or protein (NP_000000 or XP_000000), is provided relative to the genomic accession on which it is annotated. Each accession is an anchor to a menu allowing display of the sequence in several formats. Protein accessions also facilitate retrieval of specific BLink, CDD, or COG displays. Using the following figure as an example (interactive view):

Accessing the Genomic Sequence

NC_000010 is the accession of the genomic contig that contains the gene. The region being shown in this accession is indicated by the integers to the left and right of the accession. The rightward pointing arrow indicates that these mRNAs are annotated in the same orientation as the NC accession (Since this is an example of a human chromosome, pter->qter). If mRNA is annotated on the reverse complement of the genomic sequence, then the phrase (shown on reverse complement genome) is printed. RefSeq below provides a link to the RefSeq section where there may be more information about these sequences.

Clicking on the accession NC_000010 brings up a menu that facilitates navigation to:

• FASTA - the genomic sequence of the specified range, in the default orientation [not necessarily that of the annotation], in FASTA format
• GENBANK - the genomic sequence of the specified range, in the default orientation [not necessarily that of the annotation], in GenBank format
• Please note that whatever option you select, after you have navigated to Entrez Nucleotide you can select any of the display options there (Graph, XML, etc.) to customize your view.

When you have used any of the above links to display the genomic sequence of the gene displayed on the record (in this case human PAX2), you can use standard Entrez functions to:

• Download the sequence in any format using the desired combination of Display and Send to options.
• Modify the limits of the sequence to be displayed or downloaded using the Range: from ...to option.
• Add or suppress the display of optional features using the Features option.

Display of Products and Accessing their Sequences

If there are accessions listed at the left of the diagram (e.g. NM_003987, NM_003989, etc.), these represent RefSeq RNAs. Each accession anchors a link to retrieving sequence, formatted as described (FASTA, GENBANK, and GRAPHIC) for the genomic RefSeq. If there are accessions listed at the right, these are for encoded proteins. In addition to supporting links to sequence, the protein accessions facilitate connections to protein-specific tools or displays, such as

• BLink (BLAST Link), which displays the results of BLAST searches that have been done for every protein sequence in the Entrez Proteins data domain, and supports multiple tools for comparing proteins
• CDD (Conserved Domain Database), which allows review of domains found in the protein, as well as links to records of other proteins with a related domain

Each protein accession may also have a distinguishing label. In this example, these are the isoform designations, isoforms a, b, c, and d.

The labels of the RNA and protein accessions are color coded to coincide with the diagram of the placement of the exons. Blue indicates RNA, and in protein-coding genes, the untranslated region (UTR) of any exon. Maroon indicates protein, and therefore is used to represent the coding region of an exon. If an intron is flanked by coding sequence, then the line connecting the exons is maroon; otherwise, it is blue.

Genomic Context

The genomic context section reports the location of the gene on the chromosome in non-sequence coordinates and the strain and genotype information of the source sequence. The title bar of this section includes a link to Map Viewer, resulting in the same display as that generated from the Map Viewer link in the Links menu.

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.

Bibliography

The Bibliography section provides a link to PubMed in the same format as that generated from the PubMed option in the pull-down Links menu at the upper right portion of the page.

If GeneRIFs have been submitted, they are included in this section. The majority of these annotations have been provided via a collaboration between the NLM's Index Section and NCBI. The GeneRIF home page provides more information about the project, including how general users can make submissions.

Interactions

There are two major subcategories of information reported as 'Interactions'.

• HIV-1 Interactions
• General Interactions

HIV-1 Interactions

The HIV-1, Human Protein Interaction Database is funded by the Division of Acquired Immunodeficiency Syndrome (DAIDS) of the National Institute of Allergy and Infectious Diseases (NIAID) (Home). As the title indicates, this project focuses on the human proteins that have been shown to interact with proteins from HIV-1. The format of this section is different on the human and HIV-1 gene reports. On human, the display consists of:

• the HIV-1 protein, which anchors a link to Entrez gene for that gene product.
• A concise description of the interaction
• links to papers in PubMed that support the described interaction

On HIV-1, the display is subdivided by peptide name, and includes:

• a key word categorizing the interaction
• the full name of the human gene, which anchors a link to that record
• links to papers in PubMed that support the described interaction

Please note that there are separate reports from this section that are available for download, both from the HIVInteractions home page and the GeneRIF subdirectory of Gene's ftp site.

General Interactions

Interactions in this general section are reported as pairs. The report will always include the product of the gene that is part of the interaction in the first column. Depending on the type of interaction, the rest of the display may report:

• the other interactant, anchoring a link to more information
• the gene name of the other interactant, anchoring a link to that record in Entrez Gene
• the complex to which the interactant(s) belong
• the source of these data, anchoring a link to the record at that source
• a concise description of the interaction
• links to papers in PubMed that support the described interaction.

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:

1. 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. This section of the Entrez Gene report includes abbreviations indicating the level of support for assigning a GO term to a gene. Explanations for these codes are provided from the Gene Ontology site.

   Entrez Gene does not alter the associations provided by a model organism database, nor does Entrez Gene recapitulate the directed acyclic graph structure provided from GO. Thus Entrez Gene does not support retrival of all genes associated with a specific GO term based on that term's parent.

2. 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.
3. 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.
4. Markers. An enumeration of the markers that are related to this gene. The relationship is reported based either on direct reports, e-PCR using mRNA templates, or e-PCR-based localization on the genome within a region beginning 2 kb upstream of the gene and ending 0.5 kb downstream. Links are provided the NCBI UniSTS database.
5. Pathways. A description of pathways that include this gene with links to more information about that pathway.
6. Relationships. At present, used for gene models to describe some of the related sequences used to support the model transcript.

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 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 accessions and providing links to the appropriate Entrez sequence database, this section may also include descriptions of each transcript variant, accessions 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.

Related Sequences

This section lists nucleotide and protein accessions that are related to the gene, and provides links to the appropriate sequence record in Entrez nucleotide or protein. 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 using pre-calculated reports of related sequences via Entrez Nucleotide, Entrez Protein, or BLink. The sequence accessions in this section are provided for in tab-delimited format in the gene2accession.gz file in the DATA directory of Gene's ftp site.

Gene knowingly lists protein accessions 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.

The display: If the protein sequence record is not part of a set of a nucleotide record and the protein it encodes, the word 'none' is printed in the Nucleotide column. The type of nucleotide record is printed before the nucleotide accession, and the strain is printed after the protein accession, as applicable.

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 Web sites.

Tips for Previous Users of LocusLink

Table 2
Where to find the content of a LocusLink report page in Entrez Gene

LocusLink	Gene	Comments
Table of Contents	Not retained
Alphabetic lists	Not retained
Gene diagram	Transcripts and Products	Gene adds the function of Genomic context, to allow a quick view of nearby genes and links to their report pages.
Link to Evidence Viewer from Gene diagram	Evidence Viewer link in Links menu	The option to first see only the diagram of the alignment is not retained.
Button Links	Links menu	On the Gene Graphic/Default display, the number of links may be greater than in LocusLink.
Title bar with links to nomenclature source.	Initial text, with link to nomenclature source via LocusTag.	Links from LocusTag values may connect to an external database where official nomenclature has not been assigned.
OVERVIEW SECTION
RefSeq Summary	Summary	not changed
Locus type	Combination of Gene type and evidence type (under development)	The text values are not equivalent. LocusLink's Locus type values are being subdivided into Gene type and Evidence type categories.
Protein names	General protein information	not changed
Alternate symbols	Gene aliases	not changed
RELATIONSHIPS SECTION
Homology data	Links menu; HomoloGene	What is printed in LocusLink is still printed in Gene.
Related models	Related	not changed; limited to genomes being annotated by NCBI's pipeline.
FUNCTION SECTION
GeneRIFs	GeneRIFs	Not in a function section; indented under Bibliography
GO annotation	General gene information: GeneOntology	organization changed, but not content
Phenotype	General gene information: Phenotypes	organization changed, but not content
MAP SECTION
Chromosome	Genomic context	not changed
Associated markers	General gene information:Sequence Tagged Site (Markers)	Entrez Gene added display of alternate marker names.
SEQUENCE SECTION
RefSeq Sub Section
Category	RefSeq status	not changed
GenBank source	Source sequence	not changed
Domain matches	Domains	CDD link also attached to the protein accession in Transcripts and Products and in Links menu.
BL (BLink)	BLink link attached to the protein accession in the Transcripts and Products section	The function was not changed, but the placement and visibility are different.
Variant name	After the protein accession in the Transcripts and Products section	content not changed
Annotation SubSection
Genomic contig	Transcripts and Products	function retained
gb: Link to gene-specific subsequence	GENBANK view from source NC, NT, or NW accession	function retained as GENBANK option from the genomic accession-based menu.
svLink to graphic display of gene-specific subsequence	GRAPHICS view from source NC, NT, or NW accession	function retained as GRAPHIC option from the genomic accession-based menu.
mv: Map Viewer	Map Viewer in Links menu	function retained
ev: Evidence viewer	Evidence Viewer in Links menu	function retained
mm: ModelMaker	ModelMaker in Links menu	function retained
strain or haplotype	not retained
Related Sequences Subsection
Accessions, type, and strain data	Related Sequences	content not changed.
BL (BLink) from protein accessions	not retained
Additional Links	Additional Links

ASN.1 Display

The ASN.1 display provides Gene records structured according to the Entrezgene specification. An XML transformation of the ASN.1 is also provided by use of Display XML. Detailed information about the specification is provided in the For the Programmer Section.

Tips for Previous Users of LocusLink

There is no direct precedent in LocusLink. The nearest equivalent is the Save All Loci function that provides the record as text.

Display 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 For the Programmer Section.

Tips for Previous Users of LocusLink

There is no direct precedent in LocusLink. The nearest equivalent is the Save All Loci function that provides the record as text.

Display Gene Table

The Gene Table display represents the gene structure as annotated on the current genomic RefSeq representing the reference genome. It is not updated between NCBI builds. 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:

1. graphically, by repeating the display included in the Full Report
2. in a table, by reporting the position of any exon, intron, or coding region.

In addition to allowing you to browse the structure of any gene and it products, this view also makes it easier to view and download the gene-related sequence as summarized in the following table. Please note:

• If the gene has not [yet] been annotated on any of NCBI's Genomic RefSeqs, this function is not supported.
• The sequence being retrieved is from the indicated genomic sequence, not the RNA. That means that the length of a poly(A) tail is not included in the report.
• Whatever display format results from your selection, at the sequence-specific nucleotide or protein record, you can use the Display options there to generate the display option you prefer.
• Because the Gene Table reflects the annotation on the build, for bulk access you may prefer to use the seq_gene.md.gz file in the species_specific mapview subdirectory. For example:
  • Human
  • Mouse
• Because the Gene Table reflects the current NCBI batch annotation, it is possible that the RefSeq mRNAs, which are updated continuously, may have changed. Check also the Reference Sequence section of the Entrez Gene record to determine if updates have occurred (new versions and/or more variants and/or temporary suppression during a review process).

Navigation If there are multiple gene products (RNAs/proteins) annotated for a gene, navigation within the page is facilitated by the following:

• The RefSeq accessions in the first table under the graphic support jumping down to the exon report specific to that accession.
• Blue-shaded icons at the right of the RefSeq accessions repeated at the top of the exon-specific table allow you to:
  • go to the top of the page
  • go to the table for the previous product
  • go to the table for the next product

Tips for Previous Users of LocusLink

There is no direct precedent in LocusLink.

Display UI List

This display is essentially the same as that of the Brief format, with the addition of the unique identifiers 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 UI List, only the Gene identifiers are reported.

Tips for Previous Users of LocusLink

There is no direct precedent in LocusLink. The nearest equivalent is the Save All Loci function that provides the record as text.

Display LinkOut

The goal of the LinkOut feature is to facilitate access to relevant online resources beyond the Entrez system to extend, clarify, or supplement information found in the Entrez databases. Resources external to the Entrez system can submit their links as described here. Display LinkOut thus functions to show which records have supplemental information available from LinkOut providers and support connections to those providers.

Tips for Previous Users of LocusLink

There is no direct precedent in LocusLink. The nearest equivalents are the links integrated into the LocusLink record.

Display Book Links

An increasing number of Gene records are described in books and monographs provided in the Bookshelf. For sample records in this category, try the query "gene books"[filter] in the Gene query bar.

Tips for Previous Users of LocusLink

The Book Links correspond to the Books button displayed at the top of the LocusLink report page for records known to be linked to information in books in the Bookshelf.

Display GEO Links

When expression data are reported for sequences associated with a Gene record, a link to the Gene Expression Omnibus is provided. For sample records in this category, try the query "gene geo"[filter] in the Gene query bar.

Tips for Previous Users of LocusLink

There are no connections to GEO in LocusLink.

Display HomoloGene Links

These links are maintained by the HomoloGene staff, based on When expression data are reported for sequences associated with a Gene record, a link to the Gene Expression Omnibus is provided. For sample records in this category, try the query "gene geo"[filter] in the Gene query bar.

Tips for Previous Users of LocusLink

These links are the equivalent of the [H]omology button displayed from the Brief or Summary displays of query results and for the HOMOL button on the Locus Report page.

Display Nucleotide Links

The nucleotide links display option supports rapid display of the nucleotide sequence records associated with all or selected Gene records retrieved by a query. The results are displayed from Entrez Nucleotide, making it easy to format in your favorite sequence display mode.

Tips for Previous Users of LocusLink

There is no direct precedent in LocusLink. The nearest equivalents are the [G]enBank and [R]efSeq buttons displayed from the Brief or Summary displays of query results for individual records.

Display OMIM Links

The OMIM links display option supports rapid display of all or selected OMIM records associated with the Gene records retrieved by a query. The results are displayed from Entrez OMIM, making it easy to navigate to information related to diseases and disorders maintained by OMIM staff.

Tips for Previous Users of LocusLink

These links are the equivalent of the [O]MIM button displayed from the Brief or Summary displays of query results for individual records and the OMIM button on the Locus Report page.

Display Protein Links

The protein links display option supports rapid display of all or selected protein sequence records associated with the Gene records retrieved by a query. The results are displayed from Entrez Protein, making it easy to format in your favorite sequence display mode.

Tips for Previous Users of LocusLink

There is no direct precedent in LocusLink. The nearest equivalent is the [P]rotein button displayed from the Brief or Summary displays of query results for individual records.

Display PubMed Links

The PubMed Links display option supports rapid display of all or selected PubMed records associated with the Gene records retrieved by a query. The results are displayed from PubMed, making it easy to process citation information according to your favorite method.

Tips for Previous Users of LocusLink

These links are the equivalent of the [P]ubMed button displayed from the Brief or Summary displays of query results for individual records and the PUB button on the Locus Report page.

Display SNP Links

The SNP links display option supports navigation to the Summary report of variation in dbSNP for the selected gene or genes.

Tips for Previous Users of LocusLink

These links are related to that provided by the [V]ariation button displayed from the Brief or Summary displays of query results for individual record and the VAR button on the Locus Report page. There is, however, a significant difference. The report is not the summary of all variants in a gene context that is used by the link from LocusLink. Rather it is the link to all reference snp (rs) records found in a gene. To generate a gene-specific display, there are several approaches to use. One is to click on the LocusLink connection seen to the left of every Links menu, go to LocusLink, and then use the VAR button. Another approach is to open one of the rs records, scroll down to the gene-specific section, currently called LocusLink Analysis, and click on the all link.

Display Taxonomy Links

The Taxonomy links display option supports navigation to the Taxonomy database.

Tips for Previous Users of LocusLink

There was no link to Taxonomy from LocusLink.

Display UniGene Links

The UniGene links display option supports navigation to UniGene for the selected gene or genes. This link is calculated from nucleotide accessions that are associated with both resources. The UniGene cluster is also included in Gene records for vertebrate genomes, making it possible to query Gene directly by cluster.

Tips for Previous Users of LocusLink

These links are related to that provided by the [U]niGene button displayed from the Brief or Summary displays of query results for individual record and the UniGene button on the Locus Report page. Entrez Gene does add a new opportunity to retrieve UniGene links for more than one gene record at a time.

Display UniSTS Links

The UniSTS links display option supports navigation to UniSTS for the markers associated with selected gene or genes. This gene-to-marker association is calculated from reports from external databases, or by e-PCR based matches to cDNAs or annotated genes.

Tips for Previous Users of LocusLink

These links are related to individual links to UniSTS anchored by marker name on the the Locus Report page. Entrez Gene does add a new opportunity to retrieve UniSTS links for more than one gene record and more than one marker at a time.

Query tips

All functions of the Entrez indexing and query engine are used by Gene. This section will therefore summarize only how to use the tools in the context of the Gene database. General instructions for all Entrez databases are available here.

• Limits
• Preview/Index
• History
• Clipboard
• Details
• Examples
• FAQ

Limits

The limits page allows you to set the context for making queries to Entrez Gene.It is accessed from the Limits tab at the lower left in the grey query bar.

If, for example, you want to retrieve only genes encoded on plastids, you would check 'Plastids' in the Include Only section, enter your additional query terms in the Search for box, and press Go.The Limits is designed to make it easier to do the following types of queries by checking boxes, rather than writing out the text of an Entrez query. Please be reminded that Limits remain through multiple queries, unless you 'deselect' them. You can see if Limits are set on your current query result by the explicatory text in the yellow banner toward the top of the results page. You can discontinue the Limits functionality at any time by removing the check to the left of the word Limits in the query bar of a result page.

• Exclude certain genes from your result set.
  The Exclude section allows you to prevent certain types of genes from being included in your result set. Each check box is independent, so if you want to prevent retrieving both genes encoded by mitochondria and plastids, check both boxes. The NEWENTRY option refers to the GeneID used to support submission of GeneRIFs, by species, for a gene not currently in Entrez Gene. Checking All of the above prevents all in the section from being retrieved.
• Include Only certain genes in your result set.
  • 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: for which RefSeqs exist
  • NEWENTRY records: GeneIDs used to support submission of GeneRIFs, by species, for a gene not currently in Entrez Gene.
• Limit by RefSeq Status
  Retrieve genes based on the type of RefSeq used to represent the Gene.
• Limit by Taxonomy
  This set of check boxes functions to restrict the result set to the taxonomic nodes that are checked. This function to make it easier to restrict your query by organism. The limits are treated as 'Include only', and are hierarchical. So to limit your results to genes in invertebrate genomes, check 'Invertebrates'. The these selections are also treated as the boolean OR, so if you want to retrieve genes from either Danio rerio or Xenopus sp., check both Danio rerio and Xenopus.
• Field restriction This option allows you to retrieve records only when your query term exists in the selected field. These fields are the same as those described in the Preview/Index section.
• Creation date
  Retrieve records created within the range entered, or according to preselected ranges in the pull-down menu.
• Last modified
  Retrieve records modified within the range entered, or according to preselected ranges in the pull-down menu.

Examples using limits:

• retrieve non-mitochondrially encoded NADH dehydrogenases from human, mouse, or rat
  1. Use the Limits form and check human, mouse, and rat
  2. Use the Limits form and check mitochondrion under Exclude
  3. Use the Limits form to select Gene/Protein name from the All fields menu
  4. enter nadh dehydrogenase in the query box (case does not matter)
  5. Press Go.

• retrieve E. coli genes related to tryptophan
  1. Use the limits form and check Escherichia coli.
  2. enter tryptophan in the query box
  3. Press Go.

Preview/Index

The Preview/Index page on any Entrez database is a powerful resource to construct useful queries and to view terms that have been indexed under any field name. Table 4 in the previous section described the fields used in indexing the records and provided some representative queries using those fields. This section will:

1. Describe filters in general and how they can be used to find records of interest in gene.
2. Describe the properties assigned to gene records and provide examples of how to use them.

The term filter is used to describe categories of records grouped based on 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 Preview/Index under the query bar.
2. use the pull-down menu named 'All Fields' and select Filter
3. click on index button to the right of Preview to see the filter names and the number of instances of each

Filters in the Gene database are powerful tools to retrieve records of interest. For example, to retrieve all records for human genes that are associated with OMIM (i.e. have connections to OMIM) and have been annotated on the genome, use the 'AND' operator with both 'gene omim' and 'gene nucleotide pos'. The current set of filters is:

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

1. type of gene: property named as genetype name_of_type
2. source of the gene: property named as source name_of_source
3. type of RefSeq provided for the gene: property named as srcdb refseq type_of_refseq
4. other

The genetype options 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.

The other properties (i.e #4 above) are explained in the following table.

History

Use of History in Entrez Gene is consistent with all other Entrez databases. You may refer to the History section of the Entrez help documentation for more information.

Clipboard

Use of Clipboard in Entrez Gene is consistent with all other Entrez databases. You may refer to the Clipboard section of the Entrez help documentation for more information.

Details

Use of Details in Entrez Gene is consistent with all other Entrez databases. You may refer to the Details Button section of the Entrez help documentation for more information.

Examples

Constructing queries based on free text, filters, and properties can be quite powerful in retrieving records of interest from Gene. The following table summarizes some of these approaches by describing

• the intent of a query (Scope),
• how to construct a query that meets that intent (Query), and
• how usage of Gene to retrieve these data may compare to other gene-related resources, namely HomoloGene, Map Viewer, or UniGene (Notes).

Tips for the programmer

Contents:

• the Gene data model and DTD
• converting from use of LL_tmpl to Entrezgene.asn for gene-specific information.
• converting from use of the LocusLink ftp site to the Entrez Gene ftp site. The FAQ page has supplemental information.
• Entrez e-Utilities and Entrez gene

The Gene Data Model

The data model for Entrez gene is documented in the Entrezgene specification. It combines several definitions used by other NCBI databases, such as seqfeat, but also establishes definitions specific to Entrezgene. Of special note is the Gene-commentary, which is used to represent many descriptors of genes. Each Gene-commentary is defined by type, and supports specific representation of such elements as sequence database accessions (accession, version), citations (refs), external or internal resources defining the data (source), and position information. Heading, label, and text are used for general data, with the choice influenced by display in the Entrez Gene viewers.

The DTD for Gene is available from NCBI's DTD directory: /dtd/

Converting from Use of LL_tmpl

Entrezgene ::= {

Entrezgene ::= {
  track-info {
    geneid 2,

Entrezgene ::= {
  track-info {
    geneid 217346,
    status secondary,
    current-id {
      {
        db "LocusID",
        tag id 193217
      },
      {
        db "GeneID",
        tag id 193217
      }
    },

type protein-coding,

source {
    genome genomic,
    origin natural,
    org {
      taxname "Homo sapiens",
      common "human",
      db {
        {
          db "taxon",
          tag id 9606
        }
      },
      syn {
        "man"
      },
      orgname {
        name binomial {
          genus "Homo",
          species "sapiens"
        },
        lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
 Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo",
        gcode 1,
        mgcode 2,
        div "PRI"
      }
    },

homology {
    {
      type comment,
      heading "Mouse",
      label "A2m",
      text "6 62.00 cM",
      source {
        {
          src {
            db "HomoloGene",
            tag str "A2m"
          },
          anchor "A2m",
          url "/Homology/view.cgi?map=ncbi_mgd&tax_
id=10090&chr=6&symbol=A2m"
        }
      }
    }
  },

    {
      type comment,
      heading "RefSeq Status",
      label "REVIEWED"
    },

 locus {
    {
      type genomic,
      label "tat",
      accession "NC_001802",
      seqs {
        int {
          from 5376,
          to 7969,
          strand plus,
          id gi 9629357
        }
      },

   {
      type comment,
      heading "NCBI Reference Sequences (RefSeq)",
      comment {
        {
          type genomic,
          heading "Reference",
          accession "NG_002315",
          version 1,
          source {
            {
              src {
                db "Nucleotide",
                tag id 24047158
              },
              anchor "NG_002315"
            }
          },
          seqs {
            int {
              from 1,
              to 652,
              strand plus,
              id gi 24047158
            }
          }
        }
      }
    },

         products {
            {
              type peptide,
              heading "Product",
              accession "NP_000005",
              version 3,
              source {
                {
                  src {
                    db "Protein",
                    tag id 4557225
                  },
                  anchor "NP_000005",
                  post-text "alpha 2 macroglobulin precursor"
                }
              },

         comment {
            {
              type comment,
              heading "Transcriptional Variant",
              comment {
                {
                  type comment,
                  text "Transcript Variant: This variant (PAX3A) includes an
 alternate segment in the coding region, which causes a frameshift, and lacks
 several segments in the 3' coding region, compared to variant PAX3. The
 resulting protein (isoform PAX3a) has a shorter and distinct C-terminus,
 compared to isoform PAX3. Isoform PAX3a lacks the paired-type homeodomain."
                }
              }
            },

          {
              type other,
              heading "Source Sequence",
              source {
                {
                  src {
                    db "Nucleotide",
                    tag str "AJ007392,S69369"
                  },
                  anchor "AJ007392,S69369"
                }
              },

comment {
                {
                  type other,
                  heading "Domains",
                  comment {
                    {
                      type other,
                      source {
                        {
                          src {
                            db "CDD",
                            tag id 5952
                          },
                          anchor "pfam00207: Alpha-2-macroglobulin family",
                          post-text "score:2365"
                        }
                      }
                    },

     type comment,
      heading "Related Sequences",
      products {
        {
          type mRNA,
          heading "mRNA",
          accession "AY185125",
          version 1,
          source {
            {
              src {
                db "Nucleotide",
                tag id 27966960
              },
              anchor "AY185125"
            }
          },
          seqs {
            whole gi 27966960
          },
          products {
            {
              type peptide,
              accession "AAO25741",
              version 1,
              source {
                {
                  src {
                    db "Protein",
                    tag id 27966961
                  },
                  anchor "AAO25741"
                }
              },
              seqs {
                whole gi 27966961
              }
            }
          },
          comment {
            {
              type other,
              label "Strain",
              text "C57BL/6"
            }
          }
        },

gene {
    locus "A2m",
    desc "alpha-2-macroglobulin",
    ...

 gene {
    desc "spongiotrophoblast specific protein",
    maploc "17p14",
    db {
      {
        db "LocusID",
        tag id 64509
      }
    },
    syn {
      "Tpbp"
    },
    locus-tag "RGD:621454"
  },

type peptide,
              heading "Product",
              accession "NP_057236",
              version 2,
              source {
                {
                  src {
                    db "Protein",
                    tag id 7706625
                  },
                  anchor "NP_057236",
                  post-text "retinoic acid receptor, beta isoform 2"
                }
              },
              seqs {
                whole gi 7706625
              },

  syn {
      "HAP",
      "RRB2",
      "NR1B2"
    },

  prot {
    name {
      "retinoic acid receptor, beta",
      "RAR-epsilon",
      "RAR, beta form",
      "HBV-activated protein",
      "retinoic acid receptor beta 2",
      "retinoic acid receptor beta 4",
      "hepatitis B virus activated protein",
      "retinoic acid receptor, beta polypeptide"
    }
  },

      type comment,
      heading "Phenotypes",
      comment {
        {
          type comment,
          text "Cystic fibrosis",
          source {
            {
              src {
                db "MIM",
                tag id 219700
              },
              anchor "MIM: 219700"
            }
          }
        },
        {
          type comment,
          text "Pancreatitis, idiopathic",
          source {
            {
              src {
                db "MIM",
                tag id 602421
              },
              anchor "MIM: 602421"
            }
          }
        },
        {
          type comment,
          text "Sweat chloride elevation without CF",
          source {
            {
              src {
                db "MIM",
                tag id 602421
              },
              anchor "MIM: 602421"
            }
          }
        }
      }
    },

{
      type comment,
      heading "Additional Links",
      comment {
        {
          type comment,
          text "UniGene",
          source {
            {
              src {
                db "UniGene",
                tag str "Hs.411882"
              },
              anchor "Hs.411882",
              url "/UniGene/clust.cgi?ORG=Hs&CID=41
1882"
            }
          }
        },

{
      type comment,
      heading "Additional Links",
      ...
      comment {
          type comment,
          text "MIM",
          source {
            {
              src {
                db "MIM",
                tag str "602421"
              },
              anchor "602421"
            }
          }
        },

  
source {
    genome genomic,
    origin natural,
    org {
      taxname "Homo sapiens",
      common "human",
    ...
    },
    subtype {
      {
        subtype chromosome,
        name "7"
    ...

  location {
    {
      display-str "7q31.2",
      method map-type cyto
    }
  },

 {
      type comment,
      heading "Sequence Tagged Site (Markers)",
      comment {
        {
          type comment,
          source {
            {
              src {
                db "UniSTS",
                tag id 12967
              },
              anchor "D7S2742",
              post-text "(e-PCR)"
            }
          },
          comment {
            {
              type other,
              label "Alternate name",
              text "G00-674-897"
            },
            {
              type other,
              label "Alternate name",
              text "G11318"
            },
            {
              type other,
              label "Alternate name",
              text "G13271"
            },
     ...