45b6fe55c6520090418dc0d3651ecfabdb8b83de jnavarr5 Fri Aug 14 15:07:29 2026 -0700 Switch the hgdownload links to https, name the MaveDB Heatmaps track, and reflow the display conventions paragraph on the popEVE description page, refs #37791 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> diff --git src/hg/makeDb/trackDb/human/popEve.html src/hg/makeDb/trackDb/human/popEve.html index c4ac516171e..5e8b75f9832 100644 --- src/hg/makeDb/trackDb/human/popEve.html +++ src/hg/makeDb/trackDb/human/popEve.html @@ -4,37 +4,37 @@ of the variants observed in human populations, yet most have no established clinical significance. <a href="https://pop.evemodel.org/" target="_blank">popEVE</a> places missense variants on a single, proteome-wide spectrum of deleteriousness, so that variants in different genes can be compared directly. It is a deep generative model that combines cross-species evolutionary scores with human population variation: scores from EVE (an evolutionary variational autoencoder) and the ESM-1v protein language model are calibrated against allele observations in the UK Biobank using a Gaussian process, yielding a continuous, human-specific measure of variant impact. This track shows popEVE scores for all missense substitutions across roughly 18,000 human proteins. </p> <h2>Display Conventions</h2> <p> Each entry spans one protein at its genomic locus. The heatmap columns correspond to individual amino acid positions in the protein, placed at the codon's genomic coordinate. -The rows correspond to the 20 standard amino acids, ordered by amino acid class to match -the MaveDB track. Each cell -shows the popEVE score for substituting the wildtype amino acid at that position with the -row amino acid. All 19 possible substitutions are scored at each position; only the wildtype -cell is left empty. A small number of proteins, taken from an earlier data release that -provided only genomic single-nucleotide variants, show just the substitutions reachable by a -single-nucleotide change (roughly 6 of 19 per position) and therefore appear sparser. +The rows correspond to the 20 standard amino acids, ordered by amino acid class to match the +MaveDB Heatmaps track. Each cell shows the popEVE score for substituting the wildtype amino +acid at that position with the row amino acid. All 19 possible substitutions are scored at +each position; only the wildtype cell is left empty. A small number of proteins, taken from +an earlier data release that provided only genomic single-nucleotide variants, show just the +substitutions reachable by a single-nucleotide change (roughly 6 of 19 per position) and +therefore appear sparser. </p> <p> Unlike per-gene scores, popEVE is calibrated across the whole proteome, so cells are colored on a single global gradient keyed to the raw popEVE score (lower, more negative scores are more deleterious). The color is interpolated between the five anchors below: the published severe and moderate thresholds are fixed anchors, and the extremes saturate at the 0.5th and 99.5th percentiles of the proteome-wide score distribution. </p> <table style="border-collapse: collapse; border: 1px solid #ccc;"> <tr><th style="border:1px solid #ccc;padding:6px 12px;background:#f2f2f2;">Color</th> <th style="border:1px solid #ccc;padding:6px 12px;background:#f2f2f2;">popEVE score</th> <th style="border:1px solid #ccc;padding:6px 12px;background:#f2f2f2;">Interpretation</th></tr> <tr><td style="border:1px solid #ccc;background:#b2182b;width:50px;"> </td> <td style="border:1px solid #ccc;padding:4px 10px;">≤ −6.04</td> @@ -133,38 +133,38 @@ target="_blank">makedoc file</a>, and the conversion scripts are available in <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/popEve" target="_blank">our GitHub repository</a>. The strand of each protein was taken from NCBI RefSeq. The global color gradient saturates at the 0.5th and 99.5th percentiles of the proteome-wide score distribution. </p> <h2>Data Access</h2> <p>The data can be explored interactively in table format with the <a href="../cgi-bin/hgTables">Table Browser</a> or the <a href="../cgi-bin/hgIntegrator">Data Integrator</a> and exported from there to spreadsheet or tab-separated tables. From scripts, the data can be accessed through our <a href="https://api.genome.ucsc.edu" target="_blank">API</a>, track=<i>popEve</i>.</p> <p>For automated download and analysis, the genome annotation is stored in a bigBed file that can be downloaded from -<a href="http://hgdownload.soe.ucsc.edu/gbdb/$db/popEve" target="_blank">our download +<a href="https://hgdownload.soe.ucsc.edu/gbdb/$db/popEve" target="_blank">our download server</a>. The file for this track is called <tt>popEve.bb</tt>. Individual regions or the whole genome annotation can be obtained using our tool <tt>bigBedToBed</tt>, which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads" target="_blank">here</a>. +<a href="https://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads" target="_blank">here</a>. The tool can also be used to obtain features within a given range, e.g. -<tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/$db/popEve/popEve.bb -chrom=chr17 +<tt>bigBedToBed https://hgdownload.soe.ucsc.edu/gbdb/$db/popEve/popEve.bb -chrom=chr17 -start=43000000 -end=43200000 stdout</tt></p> <p>The original annotation source data can be downloaded from <a href="https://pop.evemodel.org" target="_blank">https://pop.evemodel.org</a>.</p> <h2>Credits</h2> <p> Thanks to Mafalda Dias, Jonathan Frazer, Debora S. Marks, Rose Orenbuch, and colleagues at Harvard Medical School, the Centre for Genomic Regulation, and collaborating institutions for developing popEVE and making the scores publicly available at <a href="https://pop.evemodel.org" target="_blank">pop.evemodel.org</a>. </p> <h2>References</h2> <p> Frazer J, Notin P, Dias M, Gomez A, Min JK, Brock K, Gal Y, Marks DS.