. . Interpreting Experimental Mapping Data Records MGI 5.18 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 Experiment types include Cross, RI, Hybrid, In Situ (including FISH), Contig, TEXT: Physical Mapping, TEXT: QTL, and TEXT: Radiation Hybrid.
Experiment The mapping experiment type linked to the experimental data details
Chr Chromosome
ReferenceJ number (MGI accession ID format for references), 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. Genetic Mapping Data records have the following fields:

FIELDDESCRIPTION
Experiment Type Experiment types include Cross, RI, Hybrid, In Situ (including FISH), Contig, TEXT: Physical Mapping, TEXT: QTL, and TEXT: Radiation Hybrid.
ReferenceJ number (MGI accession ID format for references), Primary author, Journal, Date, Issue, Pages)
Ref CommentComments by data editors
Experiment Name of experiment
Chromosome Chromosome
Markers Markers reported on in the experiment include: symbol, assay-type, description.

In addition, fields related to experiment type appear in query results. The fields for each experiment type appear in subsections that follow.

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Experiment Type: CONTIG

MIT created a physical map of the mouse by screening MIT primers against a large YAC library (WI/MIT-820) and building a contig map of the mouse genome. The goal was to include 10,000 markers (roughly 7000 MIT primers and 3000 STSs). This mapping information has been downloaded into MGD. To accommodate this information and make it accessible, the experiment type CONTIG has been added to the MGD mapping data set. There is one experiment per chromosome. An "experiment," in this case, consists of a set of ordered contigs assigned to a chromosome. For each contig, the following information is available:
FIELD DESCRIPTION
NameName of the contig. For example, WC11.21. Each contig name is linked to "hit" data, i.e., a record showing a correlation between STS primers and target YAC.
ChromosomeChromosome mapped by contig
Reference Accession ID Unique ID for the reference.
cM RangeEstimate of cM range covered by the contig.
STSsOrdered set of STSs. An STS may be designated by an MIT primer symbol, or GenBank ID. The STS symbol is linked to the probe record for the STS

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Experiment Type: CROSS

FIELD DESCRIPTION
MGD Accession ID Unique MGD ID assigned to an experiment record (format: MGD-CREX-####....) These numbers not assigned to new records after May 1997.
MGI Accession ID Unique ID assigned to an experiment record in MGD. Format: MGI:####, Range: 1-up. These IDs are assigned to all experiment records as of June 1997.
TypeType of cross (backcross, intercross, etc.) AND gender of F1 parent.
Female ParentGenotype of female parent.
Strain Strain of female parent.
Male Parent Genotype of male parent.
StrainStrain of male parent.
Whose CrossLast name of person or laboratory responsible for the mapping panel.
Symbols Symbols used to designate progenitor alleles.
Matrix 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.) The fields are described below:
Label Data Description
MC # Mice Number of offspring with a particular set of inherited alleles.
MC Data Line Alleles inherited in each case.
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.
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Experiment Type: RI/RC

The RI/RC Data Line represents the strain distribution pattern with respect to a particular marker in the given experiment.
FIELDDESCRIPTION
OriginProgenitor strain of the RI strain set.
DesignationRI strain set name.
Abbrev1,2Abbreviations 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.
NotesText entered by MGD editors.

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Experiment Type: IN SITU

FIELD DESCRIPTION
Band Assignment Cytogenetic position on chromosome to which marker is assigned
StrainStrain of origin of cells used in experiment
CelltypeCell type from which analyzed metaphase spreads were derived
Karyotype methodMethod used to identify chromosome bands
Robertsonian TranslocationChromosome aberration used to identify marker assignment
# metaphases analyzedNumber of metaphase spreads analyzed in experiment
total # grains scoredNumber of grains observed in experiment.
# grains correct chrom# of grains hybridizing to correct chromosomal location
Most # grains other chr(not used
Detected byHybridization detection method, either radiolabeled, or non-radiolabeled
Region/CountCytogenetic region of band assigned chr/# grains observed over that region

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Experiment Type: FISH

FIELD DESCRIPTION
Band assignment Cytogenetic band of marker
Cell typeType of cell analysed in metaphase spread
StrainMouse strain of origin for cell type
Karyotype methodMethod of staining chromosomes in the metaphase spread
Robertsonian translocationChromosome aberration used to identify marker assignment
# metaphases analyzed # of metaphase spreads analyzed in expt.
Total # Single signals# of single fluorescent signals indicating presence of marker as reported by authors
Total # Double signals# of double fluorescent signals indicating presence of marker as reported by authors
Region/Single-/Double signalsTabular representation of signals
Label Type of fluorescent label on probe

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Experiment Type: 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:

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Experiment Type: TEXT: Physical Mapping

Experimental results may be discussed in a paper but the actual data are not included in the report. In the case of Physical Mapping reports, the experimental results are given a text description. The record may include distances between markers in a tabular representation which includes the following columns:

Experiment Type: TEXT: QTL

This record contains the following fields:

Experimental results may be discussed in a paper but the actual data are not included in the report. In the case of QTL experiments, the experimental results are described in the Notes field.

Experiment Type: TEXT: QTL-Candidate Genes

This record contains the following fields:

Experimental results may be discussed in a paper but the actual data are not included in the report. Potential candidate genes reported by the authors are described in the Notes field.

Experiment Type: TEXT: Radiation Hybrid

This record contains the following fields:

Experimental results may be discussed in a paper but the actual data are not included in the report. In the case of radiation hybrid experiments, the experimental results are described in the Notes field.

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