089c09e98db52e92da694ab1a0c8891c1a7fd3e8 gperez2 Thu Apr 2 15:50:07 2026 -0700 Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM. diff --git src/hg/makeDb/trackDb/human/geneHancer.html src/hg/makeDb/trackDb/human/geneHancer.html index eae6d75cec9..419acdc1a09 100644 --- src/hg/makeDb/trackDb/human/geneHancer.html +++ src/hg/makeDb/trackDb/human/geneHancer.html @@ -77,31 +77,31 @@ Clusters composed of interactions with a single gene are colored to correspond to the gene, and those composed of interactions with multiple genes are colored dark gray.

Methods

GeneHancer identifications were created from >1 million regulatory elements obtained from seven genome-wide databases:

  1. ENCODE project Z-Lab Enhancer-like regions (version v3)
  2. Ensembl regulatory build (version 92)
  3. FANTOM5 atlas of active enhancers
  4. VISTA Enhancer Browser
    5. -
  5. dbSUPER super-enhancers
    6. +
  6. dbSUPER super-enhancers
  7. EPDnew promoters
  8. UCNEbase ultra-conserved noncoding elements

Employing an integration algorithm that removes redundancy, the GeneHancer pipeline identified ˜250k integrated candidate regulatory elements (GeneHancers). Each GeneHancer is assigned an annotation-derived confidence score. The GeneHancers that are derived from more than one information source are defined as "elite" GeneHancers.

Gene-GeneHancer associations, and their likelihood-based scores, were generated using information that helps link regulatory elements to genes:

  1. eQTLs (expression quantitative trait loci) from GTEx (version v6p)