9f9a96ab068a76799311c09a2813b0b28f8e7712 lrnassar Mon Jul 13 12:52:41 2026 -0700 Order EVE heatmap amino acid rows by class to match the MaveDB track. refs #37763 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 eve.bb; updates the makedoc, the AutoSql row label comment, and the description page. diff --git src/hg/makeDb/trackDb/human/eve.html src/hg/makeDb/trackDb/human/eve.html index 294e9ab26c5..e2e57722023 100644 --- src/hg/makeDb/trackDb/human/eve.html +++ src/hg/makeDb/trackDb/human/eve.html @@ -3,31 +3,32 @@ Missense mutations change a single amino acid in a protein and make up a large fraction of the variants observed in human populations. Most have no known clinical significance, both because clinical data are limited and because the relationship between sequence change and protein function is complex. Computational approaches that model evolutionary conservation across species can estimate how much a given position tolerates change, since residues critical to function tend to be highly conserved. EVE (Evolutionary model of Variant Effect) formalizes this reasoning with a deep generative model trained entirely on natural sequence variation, without any reliance on clinical labels. This track shows EVE scores for all possible missense substitutions in 2,949 disease-associated 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 EVE score for substituting the wildtype amino acid at that position with the row amino acid. Empty cells indicate the wildtype amino acid at a given position (no substitution) or positions for which no score is available. </p> <p> Cells are colored on a gradient: </p> <p> <span style="display:inline-block; background-color:#2166ac; width:18px; height:12px; vertical-align:middle;"></span> <b>EVE ≈ 0 — benign:</b> the substitution is well-tolerated in evolutionary sequence variation<br> <span style="display:inline-block; background-color:#f7f7f7; width:18px; height:12px; vertical-align:middle; border:1px solid #ccc;"></span> <b>EVE ≈ 0.5 — uncertain:</b> the model cannot confidently classify the variant<br> <span style="display:inline-block; background-color:#d6604d; width:18px; height:12px; vertical-align:middle;"></span> <b>EVE ≈ 1 — pathogenic:</b> the substitution is rare or absent across evolutionary sequences