MGI-Interpreting a Genes and Markers Summary

Interpreting a Genes and Markers Summary

This Help document answers the following questions about the genes and markers summary:

What determines the content of this report?
What's the difference between the narrow search and the broad search?
What should the summary report contain?
What determines the sort order on a summary page?

What determines the content of this report?

The marker summary content depends on the button you click on the Genes and Markers Query Form (cM, Nomenclature, or Genome Coordinates) and your choice in the Search box next to the Symbol/Name field. There are two types of searches: narrow and broad.

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What's the difference between the narrow search and the broad search?

The narrow search is on current gene symbols or names. The broad search includes current as well as old symbols or names, plus any synonyms, alleles, or orthologs.

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What should the summary report contain?

At the top of the Genes and Markers Query Results - Summary report is a display of your query parameters. For example:

You searched for...

Feature Type: gene

Chromosome: equals X

Genome Coordinates: between 7.4 and 7.9 Mbp

Sort: by Nomenclature

Display Limit: equals 500
Beneath the summary is an option to change your parameters. Click Modify Search to return to the Genes and Markers Query Form. You may wish to include/remove parameters or change the sorting and output defaults.

Beneath the Modify Search option is information about the amount of data found. For example:
25 matching items displayed.

If you expected more results than are displayed, click Modify Search, and change the default to No limit. Alternatively, you can type in a number that will yield fewer results.

Beneath the statement are the following columns, with a row for each matching item.

Field Description

Chr If known, the chromosome to which the marker is assigned.

cM Marker's centimorgan position. Centimorgan positions for genes and markers in MGI are based on linear interpolation using the standard genetic map described in Cox et al. (2009) (PMID). Markers without genome coordinates cannot be assigned specific cM locations and are designated as syntenic.

Genome Coordinate (strand) Marker's coordinates on the mouse genome assembly sequence map, and the strand location of the coordinates in parentheses. Plus (+) is = 5^' to 3^'. Minus (-) is 3^' to 5^'.

Feature Type Marker categories resulting from your selection(s) on the query form. For example, if you clicked Non-coding RNA gene, results for rRNA, tRNA, snRNA, snoRNA, or miRNA genes may appear.

Symbol, Name Marker symbol and name, linked to the MGI marker detail page.

Matching Text Type of information contained in the database and the text that it matches. The tool searches for items containing a match in the following order: current symbol, current name, allele symbol, allele name, withdrawn symbol, withdrawn name, human ortholog symbol, human ortholog name, other ortholog symbol.

Note: If you use the narrow search (gene symbols/names), the Matching Text field does not appear on the Genes and Markers Query Results - Summary report.

Field	Description
Chr	If known, the chromosome to which the marker is assigned.
cM	Marker's centimorgan position. Centimorgan positions for genes and markers in MGI are based on linear interpolation using the standard genetic map described in Cox et al. (2009) (PMID). Markers without genome coordinates cannot be assigned specific cM locations and are designated as syntenic.
Genome Coordinate (strand)	Marker's coordinates on the mouse genome assembly sequence map, and the strand location of the coordinates in parentheses. Plus (+) is = 5^' to 3^'. Minus (-) is 3^' to 5^'.
Feature Type	Marker categories resulting from your selection(s) on the query form. For example, if you clicked Non-coding RNA gene, results for rRNA, tRNA, snRNA, snoRNA, or miRNA genes may appear.
Symbol, Name	Marker symbol and name, linked to the MGI marker detail page.
Matching Text	Type of information contained in the database and the text that it matches. The tool searches for items containing a match in the following order: current symbol, current name, allele symbol, allele name, withdrawn symbol, withdrawn name, human ortholog symbol, human ortholog name, other ortholog symbol.

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What determines the sort order on a summary page?

The Nomenclature sort (the default) is the result of the interaction of two hierarchies: primary and secondary. The first items to appear in the summary report are any results that equal your search criteria, in secondary hierarchy order. Next all results that begin with your search criteria appear, in the same order. Finally, all results containing your criteria appear, again in the same order.
- Primary
  1. equals
  2. begins
  3. contains
- Secondary:
  1. current symbols
  2. current names
  3. allele symbols
  4. allele names
  5. old (withdrawn) symbols
  6. old (withdrawn) names
  7. synonyms
  8. human ortholog symbols
  9. human ortholog names
  10. other orthologs
The cM sort order is:
- First by chromosome.
- Second by cM position in ascending order. Markers with a syntenic cM position (or with no cM position value) appear at the end of each chromosome's list, ordered alphabetically by symbol.
Genome coordinates sort order is:
- First by chromosome.
- Second by genome coordinates.
- Third by symbol/name.

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