. . Interpreting Experimental Mapping Data Records MGI 6.10 Interpreting Maps and Mapping Data
Experimental Mapping Data Records
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This document provides a brief description of the fields and values in the query results for:

See also:

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:

FIELDDESCRIPTION
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
ReferenceJ 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.

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Mapping Data Records

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
ExperimentExperiment types include Cross, RI, Hybrid, In Situ (including FISH), TEXT: Physical Mapping, TEXT: QTL, and TEXT: Radiation Hybrid.
ChromosomeThe Chromosome for the experiment
ReferenceJ number (MGI accession ID format for references), linked to the reference abstract, Primary author, Journal, Date, Issue, Pages)
IDUnique ID assigned to an experiment record in MGI. Format: MGI:####.
Genes
GeneThe gene assayed linked to its Gene Detail page
AlleleThe allele of the gene that was used in the assay
Assay TypeA description of the assay. Examples are visible phenotype, PCR amplified length variant, and Southern analysis
DescriptionAdditional information such as a reference.
Notes
ReferenceAdditional notes from the reference
ExperimentAdditional notes about the experiment

The above fields may be present for any experiment type. Additional fields may exist for specific experiment types:

CROSS
TypeType of cross (backcross, intercross, etc.) AND gender of F1 parent.
Female ParentGenotype of female parent
StrainStrain of female parent
Male ParentGenotype of male parent
StrainStrain of male parent
Mapping PanelLast name of person or laboratory responsible for the mapping panel.
Allele 1Symbol used to designate progenitor allele for the noted strain.
Allele 2Symbol used to designate progenitor allele for the noted strain.
CROSS DataTabular 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 #miceNumber 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
OriginProgenitor strain of the RI strain set
DesignationRI strain set name
Abbreviation 1, 2Abbreviations for progenitor alleles.
RI DataThe 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
BandCytogenetic position on chromosome to which marker is assigned
StrainStrain of origin of cells used in experiment
Cell TypeCell type from which analyzed metaphase spreads were derived
Karyotype MethodMethod used to identify chromosome bands
Robertsonian Translocation Chromosome aberration used to identify marker assignment
Metaphases AnalyzedNumber of metaphase spreads analyzed in experiment
Grains ScoredNumber of grains hybridizing to correct chromosomal location
Grains on Correct ChromosomeNumber of grains hybridizing to correct chromosomal location
Region/CountCytogenetic region of band assigned chr/# grains observed over that region
FISH
BandCytogenetic region on chromosome to which marker is assigned
StrainStrain of origin of cells used in experiment
Cell TypeCell type from which analyzed metaphase spread
Karyotype MethodMethod of staining chromosomes in the metaphase spread
Metaphases AnalyzedNumber of metaphase spreads analyzed in experiment
Single SignalsNumber of single fluorescent signals indicating presence of marker as reported by authors
Double SignalsNumber of double fluorescent signals indicating presence of marker as reported by authors
LabelType 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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