MGI Glossary for unfamiliar terms (or for how MGI defines familiar terms) and acronyms
Marker Mapping Data Summaries
These pages summarize the mapping data for a marker by experimental type. MGI Marker Mapping Data Summaries have the following fields:
FIELD
DESCRIPTION
Experiment Type
The kind of mapping experiment, linked to the experimental data details. Experiment types include Cross, RI, Hybrid, In Situ (including FISH), TEXT: Physical Mapping, TEXT: QTL, and TEXT: Radiation Hybrid.
Details
More information on the experiment type, such as the type of cross, and the mapping panel used.
Chromosome
The Chromosome to which the marker maps
Reference
J number (MGI accession ID format for references), linked to the reference abstract, Primary author, Journal, Date, Issue, Pages)
The experimental data details are described below.
MGI contains genetic mapping and linkage data, including haplotype data for linkage crosses,
recombinant inbred (RI) strain distribution patterns, in-situ hybridization data, deletion mapping information, translocation breakpoint mapping, somatic cell hybrids, concordance tables, congenic strain information, and physical mapping information. Depending upon the experiment type, Mapping Data records may have the following fields:
Experiment
Experiment
Experiment types include Cross, RI, Hybrid, In Situ (including FISH), TEXT: Physical Mapping, TEXT: QTL, and TEXT: Radiation Hybrid.
Chromosome
The Chromosome for the experiment
Reference
J number (MGI accession ID format for references), linked to the reference abstract, Primary author, Journal, Date, Issue, Pages)
ID
Unique ID assigned to an experiment record in MGI. Format: MGI:####.
Genes
Gene
The gene assayed linked to its Gene Detail page
Allele
The allele of the gene that was used in the assay
Assay Type
A description of the assay. Examples are visible phenotype, PCR amplified length variant, and Southern analysis
Description
Additional information such as a reference.
Notes
Reference
Additional notes from the reference
Experiment
Additional notes about the experiment
The above fields may be present for any experiment type. Additional fields may exist for specific experiment types:
CROSS
Type
Type of cross (backcross, intercross, etc.) AND gender of F1 parent.
Female Parent
Genotype of female parent
Strain
Strain of female parent
Male Parent
Genotype of male parent
Strain
Strain of male parent
Mapping Panel
Last name of person or laboratory responsible for the mapping panel.
Allele 1
Symbol used to designate progenitor allele for the noted strain.
Allele 2
Symbol used to designate progenitor allele for the noted strain.
CROSS Data
Tabular representation of the typing of progeny resulting from the specified cross. (Note that for some experiments, matrix data are not available; in such cases, only 2 X 2 data are displayed reporting # of RIs and parentals.) Possible fields are described below:
MC #mice
Number of offspring with a particular set of inherited alleles.
2X2 Data
Tabular representation of typing of animals for specified pairs of markers.
Statistics
Tabular representation of recombination statistics for both the original cross and any additional animals typed.
RI
Origin
Progenitor strain of the RI strain set
Designation
RI strain set name
Abbreviation 1, 2
Abbreviations for progenitor alleles.
RI Data
The RI Data Line represents the strain distribution pattern with respect to a particular marker in the given experiment. Tabular display includes - Marker - RI Data Line.
Statistics
Tabular representation of recombination statistics.
IN SITU
Band
Cytogenetic position on chromosome to which marker is assigned
Strain
Strain of origin of cells used in experiment
Cell Type
Cell type from which analyzed metaphase spreads were derived
Karyotype Method
Method used to identify chromosome bands
Robertsonian Translocation
Chromosome aberration used to identify marker assignment
Metaphases Analyzed
Number of metaphase spreads analyzed in experiment
Grains Scored
Number of grains hybridizing to correct chromosomal location
Grains on Correct Chromosome
Number of grains hybridizing to correct chromosomal location
Region/Count
Cytogenetic region of band assigned chr/# grains observed over that region
FISH
Band
Cytogenetic region on chromosome to which marker is assigned
Strain
Strain of origin of cells used in experiment
Cell Type
Cell type from which analyzed metaphase spread
Karyotype Method
Method of staining chromosomes in the metaphase spread
Metaphases Analyzed
Number of metaphase spreads analyzed in experiment
Single Signals
Number of single fluorescent signals indicating presence of marker as reported by authors
Double Signals
Number of double fluorescent signals indicating presence of marker as reported by authors
Label
Type of fluorescent label on probe
HYBRID
For this type of experiment, the somatic cell hybrid data are presented in a table indicating the presence or absence of a particular marker or chromosome vs. the presence or absence of the marker being tested for linkage.
Concordance Values are given as a table with the following columns:
Chromosome/Symbol: chromosome or marker symbol
Presence (+) or absence (-) of the chromosome or marker relative to the
marker tested, expressed as: +/+, +/-, -/+, -/-
The number of occurrences for each possibility (+/+, +/-, etc.) in the
experimental data
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Experimental Mapping Data Records