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General
The "General" tab contains most of the information in RGD about the QTL. Some report pages will not display one or more of the subsections.
Symbol: The approved QTL symbol. This may be different than the symbol used in the article, but all other symbols used for this QTL will be listed in the alias symbol section.
Name: The approved full text name and number of the QTL.
Trait: The measurable phenotypic trait that has been mapped to the QTL. If multiple traits were reported in the article, only the trait with the highest statistical significance will be indicated.
Subtrait: A subcategory of the specified trait, e.g. 'diastolic' for 'blood pressure'. This allows a degree of categorization of QTLs and their traits. A more comprehensive controlled vocabulary is in development.
Method: How the trait was measured.
LOD Score: 'Logarithm of the odds' score, indicating linkage significance of two loci.
P value: The probability of obtaining a test statistic at least as extreme as the one that was actually observed, assuming that the null hypothesis is true.
Variance: A measure of the variability of a set of numbers.
Position: The chromosome and map coordinate position for the QTL in different genome assemblies are provided (three assemblies are shown here), with the source.
Cross Type: The type of cross used to determine the QTL.
Strains Crossed: The strains that were used to determine
the QTL. The strain symbols are linked to Strain reports with more
details about each strain.
Model: A link to the QTL presented in the GBrowse tool.
Annotation
The Annotation section includes subsections containing ontology
annotations assigned to the QTL. These are organized by ontology type.
Additional subsections contain information about inclusion of the QTL
in disease portals and a list of curated references for the QTL. By
default the subsections are closed to facilitate navigation through the
page but each can be expanded with a single click anywhere on the brown title
bar. Again, some report pages will not display one or more of the subsections.
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Candidate Gene Status - Lists candidate genes for the QTL with links to the gene report pages.
Disease Annotations - These annotations represent disease
to QTL 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
three-letter evidence code IAGP or IED in parentheses indicate that the
annotation is supported by data from the species specific to that gene
page.
Phenotype Annotations - These annotations represent the
association of QTLs 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.
Experimental Data Annotations - Listed are terms from five different ontologies, with the evidence code IED indicating that they were Inferred from Experimental Data. These terms were used to curate the QTL from the paper(s) originally describing it. If a disease term was used, it will be found in the "Disease Annotations" subsection. Each term links to a Term Annotation Report providing information and links about the reference used, the QTL and the ontology term, including a link to the term ontology report.
References - curated - All references connected to
annotations on the QTL 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.
RGD Disease Portals - In the “RGD Disease Portals”
subsection, Disease Portals in which the QTL appears are listed as
title/image links. Those title/image links are connected to the same
portal page as the first text link shown to the right side of the
title/image link. The text links to the right side of the title/image
links list all sections of the portal where the QTL can be found.
Related QTLs - Genetically or interactionally related QTLs are listed, with report page and reference links.
Region
Genes in Region - Lists genes in the RGSC Genome Assembly
v3.4 that overlap the region of the QTL, with descriptive information.
The data is downloadable and exportable.
Markers in Region - Lists markers in the RGSC Genome Assembly
v3.4 that overlap the region of the QTL, with descriptive information.
The data is downloadable and exportable.
Position Markers - Flanking markers are listed, with
positional and source information, and links to marker report pages.
This subsection is shown opened.
QTLs in Region - Lists other QTLs in the RGSC Genome Assembly
v3.4 that overlap the region of the QTL, with descriptive information.
The data is downloadable and exportable.
Additional Information
External Database - Links to the QTL in other databases such as Entrez Gene are provided.
Nomenclature - A history of the naming of the QTL is shown (not shown here).
RGD Curation Notes - Descriptive curator notes in several categories are listed with reference links.
