4fde51d367a488060e18e0e19d18a2594915ae76 abenetpa Thu Jul 2 14:59:11 2020 -0700 corrected typo in description refs #25815 diff --git src/hg/makeDb/trackDb/human/omimGene2.html src/hg/makeDb/trackDb/human/omimGene2.html index 0e64c48..d87b41d 100644 --- src/hg/makeDb/trackDb/human/omimGene2.html +++ src/hg/makeDb/trackDb/human/omimGene2.html @@ -1,163 +1,163 @@

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):

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, 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. The descriptions of the OMIM entries are shown on the main browser display when mousing over each entry.

Mode of Inheritance Abbreviation

Autosomal Dominant AD

Autosomal Recessive AR

Digenic Dominant DD

Digenic Recessive DR

Isolated Cases IC

Mitochondrial Mi

Multifactorial Mu

Pseudoautosomal Dominant PADom

Pseudoautosomal Recessive PARec

Somatic Mosaicism SomMos

Somatic Mutation SMu

X-Linked XL

X-Linked Dominant XLD

X-Linked Recessive XLR

Y-Linked YL

Mode of Inheritance	Abbreviation
Autosomal Dominant	AD
Autosomal Recessive	AR
Digenic Dominant	DD
Digenic Recessive	DR
Isolated Cases	IC
Mitochondrial	Mi
Multifactorial	Mu
Pseudoautosomal Dominant	PADom
Pseudoautosomal Recessive	PARec
Somatic Mosaicism	SomMos
Somatic Mutation	SMu
X-Linked	XL
X-Linked Dominant	XLD
X-Linked Recessive	XLR
Y-Linked	YL

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. +Question marks, "?", indicate 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.

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.
For each OMIM gene in the omim2gene table, the Entrez Gene ID was used to get the corresponding RefSeq Gene ID via the refLink table, and the RefSeq ID was used to get the genomic location from the refGene table.* The OMIM gene IDs and corresponding RefSeq Gene locations were loaded into the omimGene2 table, the primary table for this track.

*The locations in the refGene table are from alignments of RefSeq Genes to the reference genome using BLAT.

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