Using the Phenotypes, Alleles, and Disease Models Query Form

This help document answers the following questions:

What can I use the Phenotypes, Alleles & Disease Models Query Form to find?

Use this query form to find mutant or genetically engineered alleles, transgenes, or QTL variants by phenotype annotation, human disease annotation, nomenclature, chromosomal location, or allele categories. You can enter any combination of phenotype terms, disease terms, and accession identifiers (IDs).

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How does MGI define phenotype, disease, and allele?

phenotypeA description of the observable state of an individual with respect to some inherited characteristic. Often, individuals with different genotypes display the same phenotype. See also dominant and recessive in the MGI Glossary.
disease A human disease, syndrome, or condition described in the Disease Ontology (DO) or OMIM.
alleleOne of the variant forms of a gene, differing from other forms in its nucleotide sequence. Allele category, allele combination and allele pair also appear in the MGI Glossary.
allele nameIn MGI, an allele name is a word or phrase that uniquely identifies an allele of a given gene. The allele name has an abbreviation that is the allele symbol added as a superscript to the gene symbol. See also Gene Name in the MGI Glossary.
allele symbolIn MGI, an allele symbol is a unique abbreviation for the allele name of a given gene. Allele symbols take the form of superscripts added to the gene symbol. See also Gene Name and Gene Symbol in the MGI Glossary.
allelic composition
(genetic background)		See Allele Combination, Compound Allele Combination, in the MGI Glossary.

Note: Some terms may have unique definitions in the context of MGI queries and results. For more information, see:

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How do I fill in this query form?

  1. Enter or select values in one or more of the fields described below.
  2. Search to submit the query.
  3. Click Reset to clear the fields and return any default values.

See also:

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Is there a list of phenotype terms to select from?

Yes. There are two ways to get phenotype lists from the Phenotypes, Alleles, and Disease Models Query Form:

  1. Click Anatomical Systems Affected by Phenotypes to bring up an abbreviated list, organized roughly by system (cardiovascular, hematopoietic, and so on). The list is in alphabetical order and you can select as many terms as desired. Once you click OK, the terms populate the query box. The default relationship between the terms is OR (see What are some examples of queries and results? and Using Full-Text Searches on MGI Query Forms).
  2. Click Full Mammalian Phenotype (MP) Ontology to activate the Mammalian Phenotype Browser. Click to navigate the MP hierarchy until you find the term you are looking for. See Using the Mammalian Phenotype (MP) Browser for additional help.

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Is there a list of disease terms to select from?

Yes. To get a list of disease terms from the Phenotypes, Alleles, and Disease Models Query Form, click Human Disease (DO) to activate the Human Disease Vocabulary Browser. Navigate the vocabulary until you find the term you are looking for. See Using the Disease Ontology (DO) Browser for additional help.

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How do I make choices on the Anatomical Systems Affected by Phenotypes list?

See How do I make choices on the Anatomical Systems Affected by Phenotypes list?

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Can I query using both a phenotype term and a disease term?

Yes, you can use the Phenotype/Disease box to search for phenotypes or diseases or phenotypes and diseases. Note the following:

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What values are acceptable in each of the fields?

Mouse phenotypes | Nomenclature & location | Gene/Marker or Allele | Chromosome | cM Position | Coordinates | Categories
FIELD DESCRIPTION
Mouse phenotypes & mouse models of human disease The Phenotype/Disease box is a full-text search field. There are 5 options for entries. You can:
  1. select from the pick list of anatomical systems affected by phenotypes.
  2. browse and select Mammalian Phenotype (MP) terms or accession IDs from the full, hierarchical ontology.
  3. browse and select human disease terms from the Human Disease (DO) Vocabulary.
  4. type in your own terms connected by Boolean operators (AND, OR) and click Search. The system searches all MP annotation terms, synonyms, IDs and annotation notes as well as DO and OMIM human disease terms, synonyms, and IDs.
  5. create a query using any combination of options 1-4.

To select phenotype terms from a pick list:

  1. Click Anatomical Systems Affected by Phenotypes. The Phenotypes Selection List appears.
  2. Click high-level terms relevant to your search, such as behavior OR neurological, craniofacial, and so on. You can make multiple choices.
  3. Click Add To Query. The selections you made appear in the Phenotype/Disease box on the query form. You can edit the terms.

    Note: For details on selecting multiple terms, editing terms, and for why your selections appear as they do when they populate the Phenotype/Disease box, see Using the Phenotypes Selection List.

To select MP terms:

  1. Click Full Mammalian Phenotype (MP) Ontology. The MP ontology appears.
  2. Browse the ontology for a predefined list of Mammalian Phenotype terms and identifiers to use in your query.
  3. Copy and paste selections from the list Mammalian Phenotype Ontology and/or identifiers. Note: When using MP identifiers, be sure to include MP:. Example: MP:0005380, not 0005380.

Note: Your search term will return all genotypes annotated to a matching Mammalian Phenotype term and the related children of that matching term. For example, querying for "enlarged heart" returns genotypes annotated to cardiac hypertrophy, dilated atria, and so on.

To find mouse models associated with human diseases:

  1. enter human disease terms from the vocabulary
  2. enter DO or OMIM accession IDs
  3. type in terms and operators for a full-text search
  4. combine the options with entries in the Phenotypes box (above).

    Note: Do not use OMIM's prefix characters as part of the OMIM ID number (*, #, %, +).
    The result is a list of human disease terms, synonyms, and IDs (168600 OR Parkinson's OR DOID:14330).

How Boolean operators work:

  • Enter a single search term or multiple terms separated by AND or OR. Boolean operators must be in all capital letters.
    The distinction between an AND and an OR text search is as follows:
    • AND finds text that includes both the term before it and the term after it; for example, heart and defect finds heart defect but not heart and not defect.
    • OR finds text that includes either the term before it or the one after; for example, heart OR defect finds any text containing either heart or defect.
  • See Using Full-Text Searches on MGI Query Forms for using quotation marks, parentheses, and white space with search terms.

Nomenclature & locationSearch by symbol, name, or chromosome position. Use these parameters to expand or limit the scope of retrieved information. There are three ways to use the map position parameters (Chromosome, cM Position, Genome Coordinates). If you use Chromosome, you may also define a cM position, or genome coordinate. However, you cannot combine cM Position and Genome Coordinate with one another.

Gene/Marker or AlleleYou can search on any mouse gene or allele symbol, name, or synonym.
  • Enter one or more terms, 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: "interleukin 10 receptor, beta" or "Alpha1,4Gal-T").
Chromosome
  • Select one or more items from the chromosome selection list Use the Command key (Apple) or control key (PC) to select multiple chromosomes. Use the Shift key to make a contiguous selection, such as Chromosomes 4 - 7.
cM Position
  • Make a selection on the Chromosome list.
  • Specify a chromosomal region between two points on one chromosome selected from the Chromosome list by entering the cM values to begin and end the region, separated by a hyphen (for example, 50 - 75).
  • To limit your search to a region starting with the centromeric end, use 0 (for example, 0 - 35). To limit the region towards the distal telomere, use a large number (for example, 70 - 120).
Genome Coordinates
  • Make a selection on the Chromosome list.
  • Click the other down arrow and select either bp (base pairs) or Mbp (mega base pairs) as the unit of measurement. (The default is base pairs.)
  • Enter the coordinates as a range between two coordinates:

Examples: (be sure to select the proper unit: Mbp or bp)
  • 125618206 - 125622026
  • 125.618 - 125.622
  • 1-125618206

Notes: 

  • The build number appearing on the query form is that of the most current NCBI assembly sequence.
  • To search for alleles of markers in the pseudoautosomal region (PAR) by coordinates, select the chromosome (X or Y) to which the input coordinates correspond. To search for alleles of all markers in the PAR, select chromosome XY (without entering coordinates).
Categories

Use these check boxes to search by phenotypic allele categories and/or QTL for alleles or variants resulting in phenotypic change.

High-throughput projects have generated a large number of alleles that still exist only as cell lines. If you are interested in phenotypic alleles, then check Exclude alleles existing only as cell lines to reduce the number of results without known phenotypes.

Generation MethodMode of origin of a new allelic state.

Notes:
  • Options for searching by these allele types include spontaneous, chemically induced (ENU or other types), radiation induced, transgenic, endonuclease-mediated, gene trapped, targeted and transposon induced. See Allele Types for how MGI differentiates these categories.
  • You can exclude cell-line-only alleles from your search.
Allele AttributesThese alleles are sub-types of the various generation methods. A given allele may have more than one attribute (example: Targeted (Null/knockout, Reporter)). See Allele Types for how MGI differentiates these categories.

Note: A conditionally targeted genotype is dependent on the presence of some other factor (often a DNA sequence that expresses a protein functioning in specific recombination events). In MGI, conditional is a genotype attribute, and this is most commonly used to represent Cre-mediated excision of genomic sequences flanked by loxP sites; in most instances, this is accompanied by simultaneous insertion of some selectable marker (e.g. neomycin). The excised genotype, often associated with a phenotype, is dependent (or conditional) on the presence of the Cre-expressing construct.

Project CollectionsUse this section if you want to limit your search to alleles produced by particular institutions/projects.

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How can I find definitions for the allele categories?

See Selecting Phenotypic Allele Categories.

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Where can I find answers to questions about the summary report resulting from my query?

See Understanding Phenotypic Allele Query Summary Reports.

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Are there different ways to view the output of my query?

Yes. Click on the Allele Symbol, Chr, Category or Human Disease Models column headings or the up/down arrowheads ( ▼ ▲) to change the sort order of your results.

The results summary also allows you to export your results as tab-delimited text and spreadsheet file formats. In your search results, click on the Text File or Excel File icon. Your web browser will download a file of the results.

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How can I find more detail on my query?

On the Phenotypic Allele Query Results -- Summary page, each allele symbol and each member of an allele pair is linked to a detailed record. Click the item of interest in either the Allele column or the Allelic Composition (Genetic Background) column to see its Phenotypic Alleles Query Results -- Details page.

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Where can I find answers to questions about the detail report resulting from my query?

See Understanding Phenotypic Allele Detail Pages.

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What if my query returns no results?

If your query returns no results, the Phenotypic Alleles summary report:

The probable causes are that:

See the following for additional information:

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Can I edit my original options and requery?

Yes, you can.

If you want to edit a list or change output options:

  1. When your results appear, click the banner at the top of the page (Click to modify search). (The banner title changes to Click to hide search.) The window that appears contains your original search criteria.
  2. Make your changes.
  3. Click Search.
  4. Repeat until the desired results appear.

Notes:

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Can I use this query form to find all gene trapped alleles?

Yes. Click the gene trapped box in the Categories section of the query form.

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Where can I find answers to questions about gene trapped alleles?

See Gene Trap Questions and Answers.

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How often are annotations added?

MGI curators add new annotations from the literature every day. The MGI web site is updated with these and other new data once a week.

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What are some examples of queries using phenotypic terms?

See Using Full-Text Searches on MGI Query Forms.

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