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/TFrPeakClusters.html src/hg/makeDb/trackDb/human/TFrPeakClusters.html index dece5049c4f..32b0f53e0d1 100644 --- src/hg/makeDb/trackDb/human/TFrPeakClusters.html +++ src/hg/makeDb/trackDb/human/TFrPeakClusters.html @@ -27,31 +27,31 @@ and the total number of biosamples assayed for the protein. Links to relevant ENCODE ChIP-seq experiments and overlapping ENCODE candidate cis-regulatory elements (cCREs) are also provided.

By default, rPeaks for all 912 DNA-associated proteins with ENCODE ChIP-seq data are displayed. Users can customize the display by selecting specific DNA-associated proteins in the track settings.

Methods

2,509 ENCODE ChIP-seq experiments were integrated from 912 DNA-associated proteins across 1,152 unique biosamples to produce representative peaks (rPeaks) for each protein. The processing steps were as follows:

    -
  1. ChIP-seq peaks for each protein were downloaded from the ENCODE Portal, +
  2. ChIP-seq peaks for each protein were downloaded from the ENCODE Portal, generated using the ENCODE Transcription Factor ChIP-seq Processing Pipeline.
  3. Using bedtools merge, ChIP-seq peaks were clustered from the protein’s experiments across all biosamples.
  4. In each cluster, the peak with the highest ChIP signal (normalized by sequencing depth) was selected as the rPeak.
  5. All ChIP-seq peaks overlapping this rPeak by at least one nucleotide were marked as represented and removed from subsequent clustering rounds.
  6. Steps 2-4 were repeated until a final list of non-overlapping rPeaks was generated, representing all ChIP-seq peaks for the protein.

Data Access

The raw data for the ENCODE TF rPeak track will soon be available.

The raw data can be explored interactively with the Table Browser, for download, intersection or correlations with other tracks. To join this track with others