RGD > Help > Maps

Maps Help
Help Index
Definition
Finding info
Related info/link
Report

 
RGD Definition

"Maps are published genetic and radiation hybrid maps that order various genetic markers across the genome. RGD stores a limited number of high density public maps for use as references. Individual cross maps are not currently available."

Markers are placed on the maps with varying degrees of confidence, measured by the LOD score. Framework markers are the highest confidence markers and all other markers are 'placed' relative to these framework markers and are known as Placement markers. Placement markers are listed with the LOD score of their placement, LODs higher than 3 are indicative of high confidence positions.

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Finding Map information

1. Using the General Search

The general RGD search available at the top of each page is a quick route to finding markers and their map locations. This will search gene, marker symbols, names and aliases and results of any mapping information available on the marker. (See General RGD Search help for more information).

2. Browsing the individual maps

Quick Guide

  1. The user can view any of the available maps
  2. Each map is listed along with the number of mapped markers
  3. Selecting an individual map will bring up a list of chromosomes
  4. Selecting a chromosome will bring up the graphical map of the chromosome
  5. Click the chromosome to select a region to display in detail.

All RGD mapping data can be downloaded from RGD ftp site (http://rgd.mcw.edu/pub/data_release/MAP_DATA).

 

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Related Information/Links

The maps show the mapped markers and each marker is hyperlinked to the individual marker report. This will provide additional information on the gene, EST, SSLP, etc.

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The Map Report

Below is a description of the fields and graphics present on the Map report:

RGD: MAP Report Help

Marker Search form

A marker search box is provided on each map report. A marker name can be entered along with a bin interval and the script will find the marker's location on the current map and chromosome. The bin interval determines how much of the surrounding markers are also displayed.

Map Image

The graphical image (see example below) shows part of the FHH x ACI genetic map. The mapped markers are shown in black and red on the left side of the map, red markers are framework markers, black are placement markers.

The chromosome is divided into bins indicated by the dark and light orange bars with the cM scale running along side. Clicking the bars will bring up a Bin report listing the complete set of markers mapped in that region. Shown below is the example for the first bin on chromosome 19.

  • The marker names are hyperlinked to the marker reports.
  • If a marker has been reported as being linked to a particular gene this is listed in the Related Gene column.
  • F/P indicates if a marker is a framework or placement marker
  • LOD is the score that the marker was placed at on the map. Framework markers have a LOD of 0 on genetic maps.

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