Description

This track shows the cytogenetic locations of phenotype entries in the Online Mendelian Inheritance in Man (OMIM) database for which the gene is unknown.

Display Conventions and Configuration

Cytogenetic locations of OMIM entries are displayed as solid blocks. The entries are colored according to the OMIM phenotype map key of associated disorders:

• Lighter Green for phenotype map key 1 OMIM records - the disorder has been placed on the map based on its association with a gene, but the underlying defect is not known.
• Light Green for phenotype map key 2 OMIM records - the disorder has been placed on the map by linkage; no mutation has been found.
• Dark Green for phenotype map key 3 OMIM records - the molecular basis for the disorder is known; a mutation has been found in the gene.
• Purple for phenotype map key 4 OMIM records - a contiguous gene deletion or duplication syndrome; multiple genes are deleted or duplicated causing the phenotype.

Gene symbols and disease information, when available, are displayed on the details pages.

The descriptions of OMIM entries are shown on the main browser display when Full display mode is chosen. In Pack mode, the descriptions are shown when mousing over each entry. Items displayed can be filtered according to phenotype map key on the track controls page.

Methods

This track was constructed as follows:

• The data file genemap.txt from OMIM was loaded into the MySQL table omimGeneMap.
• Entries in genemap.txt having disorder info were parsed and loaded into the omimPhenotype table. The phenotype map keys (the numbers (1)(2)(3)(4) from the disorder columns) were placed into a separate field.
• The cytogenetic location data (from the location column in omimGeneMap) were parsed and converted into genomic start and end positions based on the cytoBand table. These genomic positions, together with the corresponding OMIM IDs, were loaded into the omimLocation table.
• All entries with no associated phenotype map key and all OMIM gene entries as reported in the "OMIM Genes" track were then excluded from the omimLocation table.

Credits

Thanks to OMIM and NCBI for the use of their data. This track was constructed by Fan Hsu, Robert Kuhn, and Brooke Rhead of the UCSC Genome Bioinformatics Group.

References

Amberger J, Bocchini CA, Scott AF, Hamosh A. McKusick's Online Mendelian Inheritance in Man (OMIM®). Nucleic Acids Res. 2009 Jan;37(Database issue):D793-6. Epub 2008 Oct 8.

Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D514-7.