Using the Genes and Markers Query Form

This help document answers the following questions:

• What can I use the Genes and Markers Query Form to find?
• How do I use this query form?
• What values are acceptable in each of the query form fields?
• How do I interpret the summary results of my query?
• How do I interpret the detail results of my query?
• How do I retrieve my results as a text file?
• Are there any sample queries?

See also:

• MGI Glossary for unfamiliar terms (or for how MGI defines and uses familiar terms) and acronyms
• General Guidelines for MGI Query Form Searches
• Genome Feature Type Definitions

What can I use the Genes and Markers Query Form to find?

Use this query form to search for detailed information on various types of mouse markers. You can:

• search for gene/marker details by entering a current or old symbol, name, allele, or ortholog; or you can restrict the search to look for only a current symbol or name.
• query by feature type and thereby confine the search to protein coding genes, to individual non-coding RNA genes, or to a variety of other categories. See Genome Feature Type Definitions for a complete list of feature types, descriptions, and corresponding SO IDs (if available/pertinent).
• retrieve lists of markers sorted by nomenclature, genome coordinates, or cM position.
• include GO classifications, InterPro domains, phenotype terms, or clone collections in your search parameters.
• limit or expand the amount of items returned.
• modify search parameters until you are satisfied with the results.
• forward results to the web, to an Excel file, or to an ftp site.

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How do I use this query form?

To search for detailed data using this query form, enter or select values in one or more of the query form fields described in the following paragraphs. After entering values in the form fields, click Search to submit the query. Click Reset to clear the fields and return any default values. See General Guidelines for MGI Query Form Searches for answers to questions about submitting queries, using operators, choosing sort orders, speeding up queries, and similar help topics.

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What values are acceptable in each of the query form fields?

Use these fields to search for genes and markers by name, location, GO terms, protein domains, for mouse phenotypes and mouse models of human disease, or by inclusion in a clone collection.

Gene/Marker | Feature Type | Map position | Gene Ontology classifications | Protein domains | Mouse phenotypes & mouse models of human disease | Clone collection | Sorting & output format

Gene/Marker	Symbol, name, or synonym for a genetic marker. Enter one or more symbols/names/synonyms (separated by commas). Note: If the term itself contains a comma, put the entire term in quotation marks to ensure that the search is on the exact phrase (example: "cyclin B1, related sequence"). By default, the search is on current and old symbols/names, synonyms, alleles, and orthologs. However, you can limit the search to current symbols or names. The operators (begins, = , ends, contains, like) present additional search options. The default is contains.
Feature Type	Use this field to query for features in a selected category. Numbers in parentheses next to each feature type indicate MGI marker totals per category. Click Show/Hide to expand/contract all list choices or click ► or ▼ open/close a category or subcategory. Click the box next to each item you wish to include in the search. Check marks indicate your choices. Mouse over a feature type to view its definition. Clicking the box beside a major category (any item that opens to subcategories, e.g., all feature types, gene, non-coding RNA gene) selects all items beneath it. A minus in a box beside a category indicates that discrete items beneath it are selected (and not the entire category or subcategory, e.g. miRNA gene and lincRNA gene and not all non-coding RNA genes). Checking all categories has the same effect as checking none of the categories. If you do not click any category, the search includes them all. An empty box indicates no choices in an entire category/subcategory. See Genome Feature Type Definitions for a table describing all choices.
Map position	Use the map position parameters ( Chromosome(s), Genome Coordinates, Cytogenetic Band, Marker Range, and cM Position) to limit the scope of your query. When using chromosome(s), you can also define genome coordinates, cytogenetic band, or cM position. You cannot combine genome coordinates, cytogenetic band, and cM position with one another. For Marker Range, you can enter any marker(s) — except QTL(s) — with coordinates. See Using Map Position Fields on MGI Query Forms for further details about entering values in these fields.
Gene Ontology classification	Genes may be described using three broad categories reflecting biological roles: Molecular Function, Biological Process, or Cellular Component. The Gene Ontology (GO) Consortium has developed structured vocabularies to specify detailed aspects within each category. MGI uses GO terms to annotate gene records. See Using Gene Ontology Classification Fields on MGI Query Forms for details.
Protein domains	InterPro Protein Domains InterPro accession ID for a protein family, domain, or functional site. To find an accession ID, click Browse InterPro protein domains. Copy and paste (or type) an ID or description into the box. To enter more than one ID or description, use AND between them. Searching on term1 AND term2 returns markers annotated to both term1 and term2.
Mouse phenotypes & mouse models of human disease	Phenotype/ Human Disease See Phenotype/Disease. Note: The query returns a marker only if at least one associated allele satisfies whatever you enter in this section.
Clone collection	Clone Collection Use this field to search for markers with at least one associated molecular segment record with an encodes or putative relationship to the marker. To restrict your search to markers with a clone ID, select one or more of the clone collections from the drop-down list. (For details such as the differences between the sets on this list, see MGI Clone Collections.) Select ANY if you do not want to restrict the search by clone collection. If you select multiple clone collections, the search returns markers with associated clones from any of the selected collections. To make multiple selections, see How do I select more than one item on a list?
Sorting and output format	Sort by Click one of the choices (Nomenclature, Genome Coordinates, or cM Position) to determine the order of any results on the summary page. The combination of sort option and search parameter affects the order and type of results listed on this summary page. If you search using current & old symbols/names, synonyms, alleles, orthologs, the summary page columns are Chr, cM, Genome Coordinates, Symbol/Name and Matching Text. If you search on current symbols/names, the summary page column headings are Chr, cM, Genome Coordinates, and Symbol/Name. Maximum Returned The default is 500. You can change this number to whatever you wish or you can click no limit.
Output	Choose from the list depending on how you wish to view the report.
Output format	Choose from the list depending on how you wish to view the results. Web (default) Web page with MGI toolbar and all the selected items. Excel Comma-delimited text in an Excel spreadsheet with a .csv (comma separated values) extension. (See http://en.wikipedia.org/wiki/Comma-separated_values for details. Tab-delimited Tab-delimited text returned to your browser with all the selected fields. Tab-delimited text to ftp site Tab-delimited text saved on our public FTP site available for 72 hours. Be sure to save the URL or print the page with the information for later access.

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How do I interpret the summary results of my query?

See Using the Marker Summary Report.

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How do I interpret the detail results of my query?

See Using the Marker Detail Report.

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What happens if I click the Your Input Welcome button on the detail page?

The Your Input Welcome button appears at the top right of your screen as part of the detailed query results. Clicking the button brings up a dialogue box to use for submitting updates and corrections to the data you are viewing. Our User Support staff will review your comments and make sure the appropriate changes are made. This provides an easy way for you to help us keep data current.

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How do I retrieve my results as a text file?

At the bottom of the form, in the Sorting and output format section, change the Output from Web (the default) to Tab-delimited.

Are there any sample queries?

The following examples show the field values that produce the given results. Default values for other fields are assumed.

1. How do I find genes with symbols/names containing cd2 mapped to Chr. 3 between 30 and 50 cM?

   Gene/Marker Symbol/Name:    cd2
   Chromosome(s):   3
   cM Position:    between 30.0-50.0
   Sort by:   cM position
   The search yields a list of at least 3 markers containing the alphanumeric cd2 on Chromosome 3.

2. Which histocompatibility markers are located on Chromosome 4?

   Gene/Marker Symbol/Name: CONTAINS histoc
   Chromosome(s): 4
   The search yields a list of at least 5 histocompatibility markers on Chromosome 4.

3. What information does MGI have on the Chrng marker?

   Gene/Marker Symbol/Name: BEGINS chrng
   This search yields a link to the marker record for Chrng (and any other markers for which the symbol or name begins with the characters chrng).

4. List all the genes on any chromosome between cM position 10 and 15.

   Chromosome(s): 2
   cM Position BETWEEN: 10.0-15.0
   Maximum returned: no limit
   Sort by: cM Position
   This query yields a listing of ~57 markers on Chromosome 2 ordered by cM position.

5. How can I find which MIT markers are located within a specific range on Chromosome 11?

   Marker Symbol/Name:    contains MIT
   Chromosome(s): 11
   Genome Coordinates: between 4.0-4.5 and change bp to Mbp
   Sort: by cM position
   This query yields a listing of ~6 MIT markers on Chromosome 11 ordered by cM position.

6. I want to find the current symbols of all non-coding RNA genes on Chr. 7 between 43 and 57 cM.

   Gene/Marker Symbol/Name    search in current symbols/names
   Feature Type:   non-coding RNA gene
   Chromosome(s): 7
   cM Position between 43 and 57
   Sort: by cM position
   Display limit equals 500
   This query returns the current symbols for at least 26 matching items that include lincRNA, miRNA, rRNA, snoRNA, and unclassified non-coding RNA gene feature types.

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