Interpreting a Genes and Markers Summary

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

See also:

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 homologs.

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What should the summary report contain?

FieldDescription
Chr If known, the chromosome to which the marker is assigned.
cMMarker'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 TypeMarker 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, NameMarker symbol and name, linked to the MGI marker detail page.
Matching TextType 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searches for items containing a match in the following order: current symbol, current name, allele symbol, allele name, withdrawn symbol, withdrawn name, human homolog symbol, human homolog name, other homolog symbol.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.

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What determines the sort order on a summary page?

  1. 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 homolog symbols
      9. human homolog names
      10. other homologs

  2. 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.

  3. Genome coordinates sort order is:
    • First by chromosome.
    • Second by genome coordinates.
    • Third by symbol/name.

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