3d194de4d74f67c1a453035e20c4769d88bec4c4 lrnassar Mon Jul 13 12:52:57 2026 -0700 Order popEVE heatmap amino acid rows by class to match the MaveDB track. refs #37791 Change the heatmap row order from alphabetical to physicochemical-amino-acid-class order (A V L I M F Y W R H K D E S T N Q G C P), matching the MaveDB Experiments heatmap so the tracks can be compared row-for-row. Rebuilds popEve.bb; updates the makedoc, the AutoSql row label comment, and the description page. diff --git src/hg/makeDb/trackDb/human/popEve.html src/hg/makeDb/trackDb/human/popEve.html index 0cca151b73c..473d820640a 100644 --- src/hg/makeDb/trackDb/human/popEve.html +++ src/hg/makeDb/trackDb/human/popEve.html @@ -4,31 +4,32 @@ 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 single-nucleotide 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 (A–Y, alphabetical). Each cell +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. Because popEVE is distributed as a list of genomic single-nucleotide variants, only amino acid substitutions reachable by a single-nucleotide change are scored; cells for substitutions requiring more than one nucleotide change, for the wildtype amino acid, or for positions without a score (for example start codons) are left empty. </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;">