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 @@ <H2>Description</H2> <!--#insert file="omimDescriptionText.html"--> <P> This track shows the genomic positions of all <B>gene entries</B> in the Online Mendelian Inheritance in Man (<A HREF="https://www.omim.org/" TARGET=_blank>OMIM</A>) database. </P> <H2>Display Conventions and Configuration</H2> <P>Genomic locations of OMIM gene entries are displayed as solid blocks. The entries are colored according to the associated <b>OMIM phenotype map key</b> (if any): <UL> <LI><B><FONT COLOR="#AAC4AA">Lighter Green</FONT></B> 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. <LI><B><FONT COLOR="#669666">Light Green</FONT></B> for phenotype map key 2 OMIM records - the disorder has been placed on the map by linkage; no mutation has been found. <LI><B><FONT COLOR="#005000">Dark Green</FONT></B> for phenotype map key 3 OMIM records - the molecular basis for the disorder is known; a mutation has been found in the gene. <LI><B><FONT COLOR="#69329B">Purple</FONT></B> for phenotype map key 4 OMIM records - a contiguous gene deletion or duplication syndrome; multiple genes are deleted or duplicated causing the phenotype. <LI><B><FONT COLOR="#BEBEBE">Light Gray</FONT></B> for Others - no associated OMIM phenotype map key info available. </UL> <P><b>Gene symbol</b>, <b>phenotype</b>, and <b>inheritance</b> 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. </P> <P> <table class="stdTbl"> <tr> <th>Mode of Inheritance</th> <th>Abbreviation</th> </tr> <tr> <td>Autosomal Dominant</td> <td>AD</td> </tr> <tr> <td>Autosomal Recessive</td> <td>AR</td> </tr> <tr> <td>Digenic Dominant</td> <td> DD </td> </tr> <tr> <td>Digenic Recessive</td> <td>DR</td> </tr> <tr> <td>Isolated Cases</td> <td>IC</td> </tr> <tr> <td>Mitochondrial</td> <td>Mi</td> </tr> <tr> <td>Multifactorial</td> <td>Mu</td> </tr> <tr> <td>Pseudoautosomal Dominant</td> <td>PADom</td> </tr> <tr> <td>Pseudoautosomal Recessive</td> <td>PARec </td> </tr> <tr> <td>Somatic Mosaicism</td> <td>SomMos</td> </tr> <tr> <td>Somatic Mutation</td> <td>SMu</td> </tr> <tr> <td>X-Linked</td> <td>XL</td> </tr> <tr> <td>X-Linked Dominant</td> <td>XLD</td> </tr> <tr> <td>X-Linked Recessive</td> <td>XLR</td> </tr> <tr> <td>Y-Linked</td> <td>YL</td> </tr> </table> </P> <P> <b>Brackets, "[ ]"</b>, before the phenotype name indicate "nondiseases," mainly genetic variations that lead to apparently abnormal laboratory test values (e.g., dysalbuminemic euthyroidal hyperthyroxinemia). </P> <P> <b>Braces, "{ }"</b>, indicate mutations that contribute to susceptibility to multifactorial disorders (e.g., diabetes, asthma) or to susceptibility to infection (e.g., malaria). </P> <P> -A <b>question mark, "?"</b>, indicates that the relationship between the phenotype and gene is provisional. +<b>Question marks, "?"</b>, 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. </P> <H2>Methods</H2> <P> The mappings displayed in this track are based on OMIM gene entries, their Entrez Gene IDs, and the corresponding RefSeq Gene locations: <UL> <LI>The data file <TT>genemap.txt</TT> from OMIM was loaded into the MySQL table <TT>omimGeneMap</TT>. <LI>The data file <TT>mim2gene.txt</TT> from OMIM was processed and loaded into the MySQL table <TT>omim2gene</TT>. <LI>Entries in <TT>genemap.txt</TT> having disorder info were parsed and loaded into the <TT>omimPhenotype</TT> table. <LI>For each OMIM gene in the <TT>omim2gene</TT> table, the <A HREF="https://www.ncbi.nlm.nih.gov/gene" TARGET=_blank>Entrez Gene ID</A> was used to get the corresponding <a href="https://www.ncbi.nlm.nih.gov/refseq/" target="_blank">RefSeq Gene ID</a> via the <TT>refLink</TT> table, and the RefSeq ID was used to get the genomic location from the <TT>refGene</TT> table.* The OMIM gene IDs and corresponding RefSeq Gene locations were loaded into the <TT>omimGene2</tt> table, the primary table for this track. </P> </UL> <P> *The locations in the <TT>refGene</TT> table are from alignments of RefSeq Genes to the reference genome using BLAT. </P> <H2>Credits</H2> <P> 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.</P> <H2>References</H2> <p> Amberger J, Bocchini CA, Scott AF, Hamosh A. <a href="https://academic.oup.com/nar/article/37/suppl_1/D793/1003813" target="_blank"> McKusick's Online Mendelian Inheritance in Man (OMIM)</a>. <em>Nucleic Acids Res</em>. 2009 Jan;37(Database issue):D793-6. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/18842627" target="_blank">18842627</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686440/" target="_blank">PMC2686440</a> </p> <p> Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA. <a href="https://academic.oup.com/nar/article/33/suppl_1/D514/2505259" target="_blank"> Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders</a>. <em>Nucleic Acids Res</em>. 2005 Jan 1;33(Database issue):D514-7. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/15608251" target="_blank">15608251</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC539987/" target="_blank">PMC539987</a> </p>