Enter a QTL symbol, alias or keyword. This tool will search the QTL symbol, name and alias (synonym) fields in the database. The asterisk '*' is an accepted wildcard. In addition, various other options are available to refine the search (See below).

Annotations

Search for QTLs based on your keyword matching curated annotations. These include free text and controlled vocabulary (Disease and Phenotype ontologies). When searching ontologies the terms' synonyms and descendant terms will also be searched.

Trait

Restrict the returned QTLs to those detected for a particular phenotypic trait. The traits currently listed are those reported by the researcher in the publication. A controlled vocabulary to describe these more uniformly is under development.

Strains

Restrict the returned QTLs to those detected using a particular strain.

Chromosome

Restrict the returned QTLs to ones mapped to a particular chromosome. The limit may also include the start and stop coordinates on the genome assembly version listed next to the input boxes.

Limit to QTLs with LOD score greater than

Restrict the returned QTLs to those with a reported LOD score of greater than the value provided.

LLimit to QTLs with P-value greater than 0 and less than 1

Restrict the returned QTLs to those with a reported P-value of less than the value provided, but between 0 and 1.

Results ordered by

• Symbol - sorts returned results alphabetically by QTL symbol
• Name - sorts returned results alphabetically by QTL name
• Chromosome - sorts returned results by chromosome (Text ordering not number)
• LOD -sorts returned results by ascending LOD score
• P-value -sorts returned results by ascending P-value
• Trait - sorts returned results alphabetically by Trait name

Results per page

Indicates the number of hits that are returned on the first results page.

The result page also lists the parameters that were used to query the database.

After you submit a query, a results page is generated displaying content related to your given search parameters. Examples of a Query Result, Select Items Report and Downloadable Report are given below.

There are several functions provided on the results page that allow the user to easily navigate through detailed information about the objects that match the search criteria.

• Select/unselect all results on current page by clicking on the check box on the header line
• Select the wanted items by checking the checkbox at the beginning of each record
• Navigate records by clicking on page number at top and bottom of the results page
• View all checked items in one page only by clicking on "View Selected" button at the bottom of the results page
• View all checked items in excel format by clicking on "Download Selected" button at the bottom of the results page
• View all items in excel format by clicking on "Download All" button at the bottom of the results page
• Go back to result summary page by clicking on "Go Back" button at the bottom of the results page

QTL Query Results Page Example:

Selected Items Report Example:

Download Report Example:

The file can be saved as an Excel file by clicking on the File button in the upper left corner of the web browser window and saved by selecting Save as type: Microsoft Excel Workbook.

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 for the QTL

Alias Symbols

Symbols that have been used to refer to this QTL in the past

Alias Name

Names that have been used to refer to this QTL in the past

Description Section:

Trait

The measurable phenotype category that was studied in the mapping of the QTL. If multiple traits were reported in the article, only the trait with the highest statistical significance will be indicated.

Other significant traits will be described in the annotation section.

Sub-trait

If applicable, a subcategory of the trait measured. For example, a QTL defined by measuring systolic blood pressure would have a Trait entry of Blood pressure and a subtrait of systolic. This allows a degree of categorization of QTLs and their traits. A more comprehensive controlled vocabulary is in development.

Description

A summary of the protocol used to determine the trait/sub-trait.

Disease Model

The human disease associated with the phenotype measured. This is a controlled vocabulary term. Clicking on the term will hyperlink to the ontology browser.

Phenotypes

A list of all the phenotypes measured. This is a controlled vocabulary term. Clicking on the term will hyperlink to the ontology browser.

Statistics

A list of all the statistics reported in the article.

Map Summary

Summary map data related to the QTL, including the chromosome where it is found, the markers defining the ends of the QTL and the peak marker.

Strains

List of strains that were used to determine the QTL. The strain symbols are hyperlinked to a Strain report with more details about the strain..

Genome Section:

View

An image of the QTL on its chromosome. The genome coordinates are also listed along with the assembly version.

Browsers

A drop down box provides hyperlinks to various genome viewing tools. The hyperlink will enter the tool with the same chromosome and coordinates as the QTL report. See the drop-down box's choice of links below.

Mapping Data

List the mapping information for the flanking and peak markers. The symbol will hyperlink to the marker's report page. The map name, chromosome, and position will hyperlink to the map viewing tool.

QTLs typically have up to three pieces of mapping information associated with them:

• Two Flanking Markers defining the limits of the QTL
• One Peak Marker, defining the position of the highest point on the probability curve (LOD plot) or smallest P-value

These are shown graphically in the example QTL diagram below:

Mapping information is shown for any or all of the flanking or peak markers that have been reported in the literature. If these markers are not present on a genetic or radiation hybrid map within RGD this is shown by the text "No mapping information available within RGD" even though these markers have obviously been mapped in the QTL study. If mapping data is available, it is linked to further information as shown below:

• Symbol - links to the main report for that object (either a gene or an SSLP report)
• Map Name - links to the Map report for that map
• Chr. (Chromosome) - links to the map for that particular chromosome
• Position - links to the map for that chromosome with the location of the particular marker highlighted in the text listing of the markers.

Annotations Section:

Annotations

Curated annotations for phenotypes, disease, candidate genes, etc. are listed in this section

Other Database Links Section:

Other database links

Contains hyperlinks to a report with all external database links and also hyperlinks directly to external databases where possible.

The new report page lists all available external database links. The new report page looks like the report below.

References Section:

References

Links to a Reference summary report. The report contains a list of the reference's RGD ID, title, citation, and hyperlinks to the RGD reference report and the Pubmed reference report.

The QTL's reference report looks like the report below.

Database Information Section:

Database Information

This section lists the RGD ID of the QTL and also has a hyperlink to the Nomenclature and Modification History report.

The QTL's Nomenclature and Modification History report looks like the report below.