e8144b87c64b0e60e475886e3ced5353f139cf43 max Fri Sep 18 07:24:42 2026 -0700 hg38 episignatures: EpigenCentral CpG probes as a second subtrack #Preview2 week - bugs introduced now will need a build patch to fix The EpigenCentral group at the Centre for Computational Medicine and the Weksberg lab, Hospital for Sick Children, publishes its curated episignatures as a track hub and asked us to host it natively instead. 15,035 CpG sites from 24 episignatures for 23 rare disorders, alongside MethaDory in the same container. The two were compiled independently and neither contains the other: 14,236 sites are in both, at identical coordinates, and 799 are only here. Built from the lab's own bigBed by makeEpigenCentral.sh, so a refresh is one command rather than the hand edits it started as. Every feature in the hub is in the track; no coordinates or values were changed. Four things were rewritten on the way in: the OMIM column went from a full URL to the entry number so trackDb builds the link, the hub's pre-rendered mouse-over column became the direction alone with the text assembled from the fields, the disorder of the strongest signature was added as its own column, and 215 rows of the per-site comparison table on 137 sites were dropped as exact duplicates, which the site's own signature count had already collapsed. Two columns were renamed to what MethaDory calls the same numbers, height to maxAbsDelta and nSignatures to sigCount. Coordinates check out two ways: 5,000 sampled sites all land on a CG dinucleotide, and every probe shared with MethaDory, which was positioned from the Illumina manifests independently, is at the same base in both. The description page keeps the structure and wording written for the hub but not its markup. Its reference table had all 24 links pointing at one PMID while displaying another, so that table is now generated from the data joined to a checked-in PMID list, each one verified against PubMed. tableBrowser is off at the request of the data providers, so Data Access points at EpigenCentral's own portal and repository. refs #38112 diff --git src/hg/makeDb/scripts/episignatures/epigenCentralRefs.tsv src/hg/makeDb/scripts/episignatures/epigenCentralRefs.tsv new file mode 100644 index 00000000000..bd60eda4490 --- /dev/null +++ src/hg/makeDb/scripts/episignatures/epigenCentralRefs.tsv @@ -0,0 +1,29 @@ +# Publication behind each EpigenCentral episignature, as listed in the lab's hub README at +# https://github.com/ccmbioinfo/EpigenCentral-UCSC-Genome-Browser +# Every PMID here was checked against PubMed esummary; EHMT1 has no PubMed record and is +# cited by DOI. Columns: signature, PMID (or empty), DOI (or empty). +#signature pmid doi +16pDel 31311581 +ANKRD11 36440975 +ARID1B 42527582 +ASXL1 35361921 +CHD7 28475860 +CHD8 31311581 +DYRK1A 34345024 +Dup7 26166478 +EHMT1 10.20517/jtgg.2020.23 +EZH2 32243864 +FHS 33909990 +HNRNPK 36130591 +KANSL1 38282074 +KMT2A 42318777 +KMT2B 42318777 +KMT2C 39013459 +KMT2D_2017 28475860 +KMT2D_2026 42134323 +MN1 40280028 +NSD1 26690673 +SMARCA2 31288860 +SRCAP 33909990 +T21 42492524 +Williams 26166478