Gene Report Page Help

Below is a description of each of the information sections available on a gene report page. Not all information will be available for every gene.

Jump to information about the:

General Summary Section
Annotation Section
Genomics Section
Sequence Section
Strain Variation Section
Additional Information Section

 

To view the "Gene Report Pages Tutorial" video click here.

For information on official rat gene nomenclature click here.

 

General Summary Section

1.  Gene Page Tabs
The "General" tab is selected by default and contains most of the information in RGD about the gene.  For genes with microarray IDs a second tab appears next to the “General” tab.  The "Array IDs" tab contains lists of microarray probe IDs associated with the gene.  Currently RGD imports probe to gene associations from Affymetrix and Ensembl.  Probe lists are separated according to the source.

2.  Gene Symbol, Name and Species
The gene symbol (official), gene name (official) and species are prominently displayed at the top of the gene page.

3.  “More on” gene box
A links box at the top right of the gene page gives one click access to information about the gene and genomic views of it in a variety of genome browsers and external database websites.  Additional external database links are available in the "Additional Information" section at the bottom of the page.

4.  RGD Object Information
The RGD ID for the gene, the date the record was created in the database, the species, the date the gene information was last updated, and the status of the record in the database appear in this box at the upper right side of the page.

5.  Description: An automated, current synopsis of specific gene information, based on annotations of the function, processes, pathways, cellular location, diseases, and phenotypes associated with the gene/gene product.  All of that information may be either experimentally derived or inferred from mouse or human orthologs.

 

6.  Type: A one word description to designate the gene as protein-coding, pseudogene, etc.  If the gene report represents a splice variant or an allele, a link to the parent gene page will be included.
RefSeq Status:
A one word code related to the NCBI RefSeq record and the GenBank sequence data that was used to provide the record. NCBI (http://www.ncbi.nlm.nih.gov/RefSeq/key.html#status)
Also known as:
Symbols and synonyms that are also used or have been used to refer to this gene.

7.  Orthologs: RGD stores data for rat, mouse and human genes and for the orthologous relationships between them for comparative purposes.  For rat, the "Orthologs" line will contain the mouse and/or human ortholog for the given rat gene with the symbol and (name) being links to the corresponding gene pages in RGD.

8.  Latest Assembly: The designation of the most current genome assembly for which RGD has data for this species is listed as the "Latest Assembly".

NCBI Annotation Information: Information about annotation oddities for a gene on the reference assembly. May be a report from NCBI’s annotation pipeline, or a comment written by a RefSeq curator to explain how a gene is (or is not) represented in NCBI’s annotation. Not provided if the RefSeq group does not provide annotation for a genome, or if there are no problems in the annotation. (http://www.ncbi.nlm.nih.gov/books/NBK3841/#EntrezGene.Summary_2)

9.  Position: Position data is presented for the latest assembly, the previous reference assembly, the cytogenetic map, and additional assemblies/maps, if available.

10.  Model: A GBrowse image (if available) for the gene, showing the intron/exon structure, and/or a “Launch Genome Browser” link is presented with one click access to this gene in RGD's GBrowse tool facilitating further exploration of the gene structure and genomic neighborhood.

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Annotation Section

The Annotation section includes subsections containing ontology annotations assigned to the gene.  These are organized by ontology type.  If a gene is not annotated to any particular ontology, the subsection for that ontology won't be displayed on that gene report page.  Additional subsections contain information about inclusion of the gene in disease portals and a list of references associated with the gene.  By default the subsections are closed to facilitate navigation through the page but each can be expanded with a single click of anywhere on the title bar.  The annotations can be viewed in "summary" mode (1) or "detail" mode (2).

 

Disease Annotations

These annotations represent disease to gene associations manually curated from the biomedical literature or imported through automated pipelines from OMIM (Online Mendelian Inheritance in Man) or GAD (Genetic Association Database). The terms come from a disease vocabulary (CTD, http://ctdbase.org/) which combines OMIM and MeSH disease vocabularies.  Disease terms followed by the evidence code IAGP, IED, IEP, or IPM indicate that the annotation is supported by data from the species specific to that gene page.  The evidence code ISS indicates that the annotation is supported by data determined for an orthologous gene in another species. An IEA evidence code indicates that the annotation was imported from an external database.

The annotation display can be toggled (by clicking on "Toggle Detail/Summary View") between “summary view” (1) and “detail view” (2).  The “summary view” lists all non-redundant annotation terms curated to this gene in alphabetical order (top to bottom, left to right). Three letter evidence codes in parentheses follow each term.  Multiple evidence codes indicates multiple annotations using the same term.  Each term is linked to an annotation details page where more details of the annotation can be found (sample).

Toggling the annotation display to “detail view” (2) reveals the annotations in table form, where all details are shown on a single line:

Term: Ontology term (In this case a disease vocabulary term.)

Qualifier: A descriptive word or phrase adding detail to the gene/term association.

Evidence: A three letter code which labels the annotation based on what evidence exists for that gene/term association (evidence code guide).

With: A database ID which identifies a second gene or an ortholog which is the basis for the annotation or the evidence.

Reference: The literature reference from which the annotation originated, or the reference number for the automated pipeline that imported the annotation.

Notes: Additional information identifying external database information associated with an imported annotation or additional information added manually to enrich the annotation is found here.  For disease annotations the notes field may contain a note with a specific meaning defined by this structure: “associated with (a second disease term)";molecular level of gene/gene product affected in the disease:nature of gene/gene product alteration:tissue/cellular/genomic location of alteration:specific mutation or SNP nomenclature associated with alteration (species or strain identity).


Gene-Chemical Interaction Annotations

These annotations are imported from the Comparative Toxicogenomics Database (CTD).  In the "Summary View" only the chemical name and evidence code are shown. In the "Detail View" shown here, more information can be seen, including the interaction term in the "Qualifier" field and the interaction sentence in the "Notes" field.

Gene Ontology Annotations

These annotations represent gene product/molecular function, gene product/biological process, and gene product/cellular component associations. The terms come from the Gene Ontology Consortium (www.geneontology.org). Gene Ontology (GO) terms followed by the evidence code IDA, IEP, IMP, TAS, or NAS indicate that the annotation was manually curated from the scientific literature.  The evidence code ISS, ISO, IBA, IBD, IKR, or IRD indicates that the annotation is supported by data determined for an orthologous gene in another species. An IEA evidence code indicates an unreviewed annotation that was imported from an external database.

This example shows GO annotations in the summary view. 

 


Molecular Pathway Annotations

These annotations represent the association of gene products to molecular pathway processes.  The terms come from the Pathway Ontology (PW) created at RGD (http://database.oxfordjournals.org/content/2011/bar010.long).  The terms are supported by the same group of evidence codes as used for Gene Ontology annotations.  As indicated in the 'Source' column, annotations are either generated at RGD, or are imported via mapping to RGD PW terms from the Pathway Interaction Database (PID; http://pid.nci.nih.gov/)  or the Kyoto Encyclopedia of Genes and Genomes (KEGG; http://www.genome.jp/kegg/). This example shows PW annotations in the detail view. 

External Database Links: These Molecular Pathway Annotations subsections may also contain a list of links to related pathway diagrams at PID and KEGG.
   


Phenotype Annotations

These annotations represent the association of genes with particular phenotypes.  The terms come from the Mammalian Phenotype Ontology (MP) developed at MGI (http://www.informatics.jax.org/, Genome Biol. 6(1):R7. Epub 2005 Dec 15.) The terms are supported by the same group of evidence codes as used for Disease vocabulary annotations.  This example shows MP annotations in the summary view.


RGD Disease Portals

Gene report pages link to each Disease Portal in which that gene appears.  In the “RGD Disease Portals” subsection portals are listed as title/image links.  Those title/image links are connected to the same portal page as the first link shown to the right side of the title/image link.  The text links to the right side of those title/image links list all sections of the portal where the gene of that particular report page can be found.    In the case shown here, Cd36 appears in the Diseases, Phenotypes, and Biological Process sections of the RGD Cardiovascular Disease Portal.  This means Ptgs1 is annotated to one or more cardiovascular Disease vocabulary terms, Mammalian Phenotype Ontology terms, and Biological Process GO terms related to cardiovascular diseases.


 

 

References – curated

All references connected to annotations on the gene report page are listed here. Citations link to RGD Reference report pages which in turn link to PubMed in most cases.  For more information about RGD Reference Reports, click here




References – uncurated

These references are associateded with the gene report page by automated downloads from Gene at NCBI.  The list consists of PubMed IDs, which link to abstracts at PubMed.
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Genomics Section

The Genomics Section contains information about the gene's sequence, position and genomic neighborhood. In addition, here you will find information about what other data objects, such as QTLs, strains and markers, the gene has been linked to in the literature.

Candidate Gene Status

In cases where a researcher designates one or more genes as candidates for a Quantitative Trait Locus (QTL), RGD curators make an association between the gene(s) and the QTL.  This association is shown on both the gene and QTL pages.  Here Cyp11b1 has been designated as a candidate gene for two QTLs, Bp61 and Bp336.

The QTL symbol links to the RGD QTL record, simplifying access to the QTL record for more information about that QTL.

Comparative Map Data

The map data from the “Position” section of the gene report page is repeated here along with the equivalent data from the associated orthologs. The name of the current reference assembly for each species is shown in bold blue font.


Markers

Curated markers which have been linked to the gene in the literature are listed here.  All of the position data which is available in the RGD database is displayed for each marker.  The name of the current reference assembly is shown in bold blue font.


QTLs in Region 

The table lists all QTLs which overlap the position of the gene in the current reference assembly.  The data includes statistics (LOD and P value), Trait and Subtrait names, Chromosome location, and Genomic coordinates (Start and Stop).

The "Full Report" link takes users to the list in the RGD Search Results format which includes links to the QTL report pages and the ability to change the assembly for which position information is displayed.

The "CSV" and "TAB" links download the list of QTLs in either comma separated (CSV) or tab-delimited (TAB) format, ready to be saved to your computer and/or sent to other tools for further analysis.

"Printer" allows users to print the list of overlapping QTLs.

"GViewer" sends the list of QTLs to the RGD Genome Viewer tool where you can see them in the context of the entire genome (GViewer).  Use the GViewer's "Add Objects" function to add and see the exact position of the gene with respect to these overlapping QTLs (GViewer help link goes here).


Related Rat Strains

Strains which have been linked to the gene in the literature. For example, congenic strains which contain the gene, are listed.  Strain symbols are linked to the corresponding strain report pages.


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Sequence

The Sequence section contains information about the gene's nucleotide and protein sequences.

Nucleotide Sequences

This is a list of all NCBI RefSeq and GenBank nucleotide accession numbers  associated with this gene.  Each accession number is a link to its page in the Nucleotide database at NCBI. The “Get FASTA” and “Search GEO for Microarray Profiles” links also lead to corresponding pages in an NCBI database.

Reference Sequences: These are NCBI reference sequences (RefSeqs, http://www.ncbi.nlm.nih.gov/RefSeq/) associated with this gene.  RefSeq accession numbers include those that begin with NM, NR, XM, or XR for nucleotide sequences.  RefSeq Status: A one word code related to the NCBI RefSeq record and the GenBank sequence data that was used to provide the record (http://www.ncbi.nlm.nih.gov/RefSeq/key.html#status).  Type: Designation as coding or non-coding  Position: Data is presented for sequence used at NCBI in determining the RefSeq.  The name of the current reference assembly is shown in bold blue font.

 


Protein Sequences

This is a list of all NCBI RefSeq and GenBank protein accession numbers associated with this gene.  Each accession number is a link to its appropriate page in the Protein database at NCBI. Each “Get FASTA” link also leads to the corresponding page in the Protein database at NCBI.

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Strain Variation Section

The Strain Variation section contains data on strain-specific variations discovered through genomic sequencing of specific strains.  Currently, data is available for three strains:  FHH, SS and SHR.

This is a listing of all SNPs which are located in the position of the gene in the current reference assembly.
"CSV" and "TAB" links download the list of SNPs in either comma separated (CSV) or tab-delimited (TAB) format, ready to be saved to your computer and/or sent to other tools for further analysis.
"Printer" allows users to print the list of variant data.
Start” gives the nucleotide location of the SNP, while “Stop” gives the coordinate immediately downstream of the SNP.
Both the reference and variant nucleotide are listed.
Depth: Sequencing coverage which supports this variant.
Allele Frequency: A value that is based on the confidence level with which the variant SNP is called.  A value of ≥ 10 is needed to confidently call a SNP.
Zygosity: This label of homozygous (100%), possibly homozygous (86-99%), or heterozygous (≤ 85%) is based on the percentage of reads in which the variant SNP is called.

Amino Acid Change

If the SNP is in an exon, the effect on the amino acid is displayed with separate information.  The source transcript is given as a GenBank accession number, the amino acid change type is identified as “synonymous” or “nonsynonymous”, the reference and variant amino acids are given as the amino acid one letter codes,
"Near Splice Site" indicates whether (T) or not (F) the variant SNP is within 10 bp of a splice site, and
Polyphen Prediction (Polymorphism Phenotyping) is an algorythmic analysis of the variant which determines the variant to be "Possibly damaging", "Probably damaging", "Benign", or "N/A".

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Additional Information Section


External Database Links

This list displays many different web sites with links to web pages with additional information about the gene/gene product(s) which is the subject of this gene report page.                                                                                                                          
 

Nomenclature History

This is a chronological record of all the changes in symbol and name that have occurred for this gene, since the gene report was entered into the database. 
Description: A brief explanation of the changes made on the given date.   
Status: A one word descriptor to indicate whether the nomenclature is/was approved or provisional.


RGD Curation Notes

These are legacy annotations made to genes before the use of ontology terms was adopted at RGD.  Some of this information may be replicated in the Annotation section of the gene report.

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