df99c448f8e0386bb718da0044b22752fc145713 gperez2 Thu Jun 4 00:15:12 2026 -0700 Updating ENCODE4 Regulation labels and description pages for hg38 and mm10. refs #34923 - Capitalized 363 hg38 Layered organ shortLabels and shortened the over-length TF rPeaks and Indiv. composite longLabels; updated the mm10 TF ChIP container longLabel. - TF rPeaks: added the missing SHOX2 to filterValues.factor (now 912), and updated "911 factors"/"2,502 experiments" to "912"/"2,509". - Supertrack pages: changed Layered bullets from "highlights" to "displays", reworded the histone and CTCF bullets, updated the default-organ note, and updated stale hg38 organ counts to 38/41/26/38/36. - Updated the TF ChIP facet name "Tf" -> "TF" on both description pages. - Makedoc: updated hg38 "911-factor" -> "912-factor" and mm10 RNA-seq Unstranded "26" -> "8". diff --git src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfPeaks.html src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfPeaks.html index b040c8fd4c3..fb9e60a7dde 100644 --- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfPeaks.html +++ src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfPeaks.html @@ -51,36 +51,36 @@ Shade of lowest-scoring items setting can darken them for easier visibility. Note: Increasing the shade reduces the visible contrast between low and high scoring peaks.

If the rPeak overlaps a cognate TF motif site from the collection in Andrews et al., 2023, the motif site is colored green using decorators.

Clicking on an rPeak provides detailed information about the biosamples where the rPeak was detected, including the count of biosamples with contributing ChIP-seq peaks, the total number of biosamples assayed for the protein, and a per-biosample table listing each contributing experiment with its ENCODE accession. The protein name links to Factorbook, and overlapping ENCODE candidate cis-regulatory elements (cCREs) link to SCREEN.

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By default, rPeaks for all 911 DNA-associated proteins with ENCODE ChIP-seq data are +

By default, rPeaks for all 912 DNA-associated proteins with ENCODE ChIP-seq data are displayed. A filter is available to select specific proteins.

Methods

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2,502 ENCODE ChIP-seq experiments were integrated from 911 DNA-associated proteins across +

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