4a646e64a0e5a56c6dfd9cd097538f1e44edf2e5 abenetpa Fri May 29 19:40:03 2020 -0700 added explanation brackets, braces, question mark to display conventions refs #18419 diff --git src/hg/makeDb/trackDb/human/omimGene2.html src/hg/makeDb/trackDb/human/omimGene2.html index c401e09..1a9ba06 100644 --- src/hg/makeDb/trackDb/human/omimGene2.html +++ src/hg/makeDb/trackDb/human/omimGene2.html @@ -1,46 +1,61 @@

Description

This track shows the genomic positions of all gene entries in the Online Mendelian Inheritance in Man (OMIM) database.

Display Conventions and Configuration

Genomic locations of OMIM gene entries are displayed as solid blocks. The entries are colored -according to the associated OMIM phenotype map key (if any): +according to the associated OMIM phenotype map key (if any):

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.
Light Gray for Others - no associated OMIM phenotype map key info available.

Gene symbol and disease information, when available, are displayed on the details page for an -item, and links to related RefSeq Genes and UCSC Genes are given. +

Gene symbol, phenotype, and inheritance information, when available, are +displayed on the details page for an item, and links to related RefSeq Genes and UCSC Genes are +given. +

+Brackets, "[ ]", before the phenotype name indicate "nondiseases," mainly genetic variations that +lead to apparently abnormal laboratory test values (e.g., dysalbuminemic euthyroidal +hyperthyroxinemia). +

+Braces, "{ }", indicate mutations that contribute to susceptibility to multifactorial disorders +(e.g., diabetes, asthma) or to susceptibility to infection (e.g., malaria). +

+A question mark, "?", indicates that the relationship between the phenotype and gene is provisional. +More details about this relationship are provided in the comment field of the map and in the gene +and phenotype OMIM entries.

The descriptions of the 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

The mappings displayed in this track are based on OMIM gene entries, their Entrez Gene IDs, and the corresponding RefSeq Gene locations:

The data file genemap.txt from OMIM was loaded into the MySQL table omimGeneMap.
The data file mim2gene.txt from OMIM was processed and loaded into the MySQL table omim2gene.
Entries in genemap.txt having disorder info were parsed and loaded into the omimPhenotype table.