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This help document answers the following questions:

• What can I use the Mammalian Orthology query form to find?
• How do I fill in this query form?
• What values are acceptable in each of the query form fields?
• How do I interpret the results of my query?
• Are there any supporting references?
• Are there any comparative maps?
• Are there any examples of queries and results?

See also:

• MGI Glossary for unfamiliar terms (or for how MGI defines specific terms) and acronyms.
• General Guidelines for Searching MGI

What can I use the Mammalian Orthology query form to find?

The Mammalian Orthology query form enables you to search for orthologies between two or more mammalian species. The form is divided into two sections: Primary Species and Comparison Species. Using Primary Species options, you can create a very focused search by specifying details for comparison. For example, you can choose Human and search for orthologies to human chromosome 10 and cytogenetic band beginning with q21.

An important search option (located at the top of the form) is include in results either only selected species or all Orthologous species for comparison. By default, only orthologies for the selected species appear for the query. If you select all Orthologous species, the search returns not only orthology records that fit your search criteria exactly but also orthologies from unspecified species that also meet the same search criteria.

The query results provide a tabular display of orthology classes. A class is a set of orthologous markers.

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How do I fill in 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 Using MGI Query Forms for answers to questions such as:

• How do I submit a query?
• What are operators and how do they affect my query? (See also Using Operators on MGI Query Forms)
• Does it matter what case I use when I type values in the fields?
• How do I select more than one item on a list?
• How do the sort options work?
• Is there a maximum number of results I can get back all at once?
• How can I speed up a query?

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

Primary Species | Marker Symbol/Name | Chromosome | Cytogenetic Band | Author | Reference Accession ID | Marker Accession ID | Comparison Species

FIELD	DESCRIPTION
Primary Species	A selection list of mammalian species that the database contains orthology information about. (The Comparison Species field is similar.) Select ANY to search for all orthologies with the specified characteristics (chromosome, cytogenetic band) in any species, or select one species from the list. When you specify both primary and comparison species, e.g., mouse and human, the search finds all orthologies for both mouse and human satisfying any other criteria you specify on the query form. By default, only orthologies for the selected species appear. You can select the option (at the top of the form) to Include in results all orthologous species. The most frequently used species, mouse and human, are at the top of the list. Other species appear in alphabetical order.
Marker Symbol/Name	Symbol, name, or synonym for a mouse 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 symbols/names and synonyms. However, you can limit the search to current symbols (no search of gene names) or to current symbols/names only (no synonyms). The operators (begins, = , ends, contains, like) present additional search options. The default is contains. To exclude symbols from a search, click NOT, select an operator, enter the symbol, and set the search criteria. Note: Many genes have withdrawn symbols and synonyms. If you click NOT and use the default setting, a gene appears if any of its symbols (including withdrawns and synonyms) do not match the query. Therefore, in apparent contradiction of your intent, some genes appear whose current symbol matches the query. You may find it more useful to change the selector to current symbols when using the NOT operator.
Chromosome	A text entry field for a chromosome in the primary (or comparison) species. Enter the number or character designation for one or more chromosomes. The default operator is = (equals). Enter one or more chromosomes. Use commas between multiple entries. The operator you select applies to all entries.
Cytogenetic Band	A text entry field for a cytogenetic band region in the primary (or comparison) species.
Author	Author names are stored in PubMed format: last name, space, first and second initials, as in Zhivago DE. The default operator is CONTAINS. Enter a part or all of the name of the author you are interested in. If you use =, you must type the name precisely as it is stored in the database. Combining LIKE with a wildcard or clicking the NOT checkbox to exclude an author from a search may also prove useful.
Reference Accession ID	A unique ID assigned to the article referenced in MGI. Search by MGI Accession ID, J number, or PubMed ID. Enter a single ID, multiple IDs separated by commas, or a range of IDs. See Using the Accession IDs Query Form for details. When you search for orthologies using this field, the system searches for all orthology records associated with the article referenced.
Marker Accession ID	A unique ID assigned to a marker symbol. You can search using, for example, the MGI Accession ID, the MGD Accession ID, the EC number, and so on. Enter a single ID, multiple IDs separated by commas, or a range of IDs. See Using the Accession IDs Query Form for details. When you search for orthologies using this field, the system searches for all MGI orthology records associated with the marker referenced by the given Symbol Accession ID.
Comparison Species	See Primary Species.
Chromosome	See Chromosome.
Cytogenetic Band	See Cytogenetic Band.

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Are there any examples of queries and results?

1. List the orthologies between markers on mouse chromosome 6 and any chromosomes in human.

   Sort by: chromosomal location in primary species Primary species: mouse, laboratory (Mus musculus/domesticus)
   Chromosome = 6
   Comparison species: human (homo sapiens)
   This search yields over 100 orthology classes. Each includes a mouse marker located on Chromosome 6 and a human orthology to that marker.

2. Compare a region of human chromosome 12, on the q arm near band 12, with mouse.

   Chromosome = 12
   Cytogenetic band BEGINS q12
   Comparison species = mouse, laboratory (Mus musculus/domesticus)
   This search yields several sets of orthologies. Each set contains a human marker located on Chromosome 12 at some position on the q arm starting with q12 and a mouse marker orthologous to it.

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