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 @@ <b>Shade of lowest-scoring items</b> setting can darken them for easier visibility. <b>Note:</b> Increasing the shade reduces the visible contrast between low and high scoring peaks.</p> <p>If the rPeak overlaps a cognate TF motif site from the collection in Andrews et al., 2023, the motif site is colored <span style="color:#36DD81; font-weight:bold;">green</span> using decorators.</p> <p>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 <a target="_blank" href="https://factorbook.org">Factorbook</a>, and overlapping ENCODE candidate cis-regulatory elements (cCREs) link to <a target="_blank" href="https://screen.wenglab.org">SCREEN</a>.</p> -<p>By default, rPeaks for all 911 DNA-associated proteins with ENCODE ChIP-seq data are +<p>By default, rPeaks for all 912 DNA-associated proteins with ENCODE ChIP-seq data are displayed. A filter is available to select specific proteins.</p> <h2>Methods</h2> -<p>2,502 ENCODE ChIP-seq experiments were integrated from 911 DNA-associated proteins across +<p>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:</p> <ol> <li>ChIP-seq peaks for each protein were downloaded from the <a target="_blank" href="https://www.encodeproject.org">ENCODE Portal</a>, generated using the <a target="_blank" href="https://www.encodeproject.org/chip-seq/transcription_factor/">ENCODE Transcription Factor ChIP-seq Processing Pipeline</a>.</li> <li>Using bedtools merge, ChIP-seq peaks were clustered from the protein’s experiments across all biosamples.</li> <li>In each cluster, the peak with the highest ChIP signal (normalized by sequencing depth) was selected as the rPeak.</li> <li>All ChIP-seq peaks overlapping this rPeak by at least one nucleotide were marked as represented and removed from subsequent clustering rounds.</li> <li>Steps 2-4 were repeated until a final list of non-overlapping rPeaks was generated,