d2a02f56a0e84d51213d44955b694ce7daace230
jnavarr5
Fri May 31 11:41:50 2019 -0700
Updating redirected links for hg18, uiLinks cronjob.
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Description
This track shows the cytogenetic locations of phenotype entries in the Online Mendelian
-Inheritance in Man (OMIM) database for which
+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.
PMID: 18842627; PMC: PMC2686440
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.
PMID: 15608251; PMC: PMC539987