991d6b875ab1bb832434ca3f939ff77de3d6d786 jnavarr5 Thu Nov 13 14:59:51 2025 -0800 Updating the track descripiton page since the g2p track isn't just about DDG2P, refs #36469 diff --git src/hg/makeDb/trackDb/human/g2p.html src/hg/makeDb/trackDb/human/g2p.html index 04825953af6..b7f0451b280 100644 --- src/hg/makeDb/trackDb/human/g2p.html +++ src/hg/makeDb/trackDb/human/g2p.html @@ -1,85 +1,88 @@ <h2>Description</h2> <p> -These tracks display genes associated with severe developmental disorders. The track can be used to -filter genomic sequencing data from individuals with genetic disorders to identify likely causative -variants and accelerate diagnosis. +This track displays detailed, evidence-based gene-disease models, curated from the literature by +experts. The track can be used to filter genomic sequencing data from individuals with genetic +disorders to identify likely causative variants and accelerate diagnosis. More information about +the G2P project can be found on the +<a href="https://www.ebi.ac.uk/gene2phenotype/about/project" target="_blank">Gene2Phenotype</a> +website. </p> <h2>Display Conventions and Configuration</h2> <p> For each track, items are colored according to the likelihood that the gene-disease association is true:</p> <ul> <li> <font style="color: rgb(39,103,73);"><b> Dark-green</b></font> - Definitive</li> <li> <font style="color: rgb(56,161,105);"><b>Green</b></font> - Strong</li> <li> <font style="color: rgb(104,211,145);"><b>Light-green</b></font> - Moderate</li> <li> <font style="color: rgb(252,129,129);"><b>Pink</b></font> - Limited</li> <li> <font style="color: rgb(229,62,62);"><b>Red</b></font> - Disputed</li> <li> <font style="color: rgb(155,44,44);"><b>Dark-red</b></font> - Refuted</li> </ul> <p>Each <b>mouseover</b> tooltip provides the following information:</p> <ul> <li><strong>G2P ID</strong>: Unique identifier assigned by the Gene2Phenotype (G2P) database.</li> <li><strong>Variant Consequence</strong>: Predicted effect each allele of a variant has on a transcript.</li> <li><strong>Disease Name</strong>: Name of the disease associated with the variant.</li> <li><strong>PubMed IDs</strong>: Publications associated with the variant.</li> <li><strong>Molecular Mechanism</strong>: Description of the molecular processes and interactions causing pathogenic effects.</li> <li><strong>Allelic Requirements</strong>: Number of alleles required at a locus to produce a pathogenic phenotype (e.g., monoallelic, biallelic).</li> <li><strong>Date of Last Review</strong>: Most recent date the entry was manually reviewed.</li> </ul> <h2>Method</h2> <p> Expert-curated gene disease models released by the Gene2Phenotype project were imported and processed to create a BED-based track annotating genomic regions reported to be associated with disease in the literature. Standard genome assembly coordinates and gene annotations were used to map entries to the browser. </p> <h2>Contact</h2> <p> For more information on the Gene2Phenotype project, please contact <A HREF="mailto:g2p-help@ebi. ac. uk"> g2p-help@ebi. ac. uk</A> <!-- above address is g2p-help at ebi.ac.uk --> </p> <h2>Data Access</h2> <p> Source data for these tracks are available directly from <a href="https://www.ebi.ac.uk/gene2phenotype/" target="_blank">Gene2Phenotype</a>. </p> <h2>References</h2> <p> Thormann A, Halachev M, McLaren W, Moore DJ, Svinti V, Campbell A, Kerr SM, Tischkowitz M, Hunt SE, Dunlop MG <em>et al</em>. <a href="https://doi.org/10.1038/s41467-019-10016-3" target="_blank"> Flexible and scalable diagnostic filtering of genomic variants using G2P with Ensembl VEP</a>. <em>Nat Commun</em>. 2019 May 30;10(1):2373. DOI: <a href="https://doi.org/10.1038/s41467-019-10016-3" target="_blank">10.1038/s41467-019-10016-3</a>; PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/31147538" target="_blank">31147538</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6542828/" target="_blank">PMC6542828</a> </p> <p> Yates TM, Ansari M, Thompson L, Hunt SE, Uhalte EC, Hobson RJ, Marsh JA, Wright CF, Firth HV. <a href="https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-024-01398-1" target="_blank"> Curating genomic disease-gene relationships with Gene2Phenotype (G2P)</a>. <em>Genome Med</em>. 2024 Nov 6;16(1):127. DOI: <a href="https://doi.org/10.1186/s13073-024-01398-1" target="_blank">10.1186/s13073-024-01398-1</a>; PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/39506859" target="_blank">39506859</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11539801/" target="_blank">PMC11539801</a> </p>