66fafe88184bb3a8a45a50026f4d6c7fbbc24109 markd Tue Sep 29 10:12:53 2026 -0700 Rebuild the TSS tracks as traditional composites, for wiggle control. refs #35528 A faceted composite is routed to facetedCompositeUi(), which returns before cfgByCfgType(), so it never draws the wiggle controls: no data view scaling, no viewing range, no windowing function, no track height. Signal tracks need those, so proCapNet and encode4ProCap are now traditional composites. They stay separate composites under the TSS container. The multiWig strand overlays survive the change. The old comment here claimed a multiWig under a plain composite "is flattened away and never drawn"; that is wrong for drawing, which #36320 fixed. Only the hgTrackUi subtrack list flattens, because compositeUiSubtracks() walks to leaves, so the overlays get no inline config block and are configured from their own pages. Raised as #38441. The matrix has to be declared over the leaves, since that is the level hgTrackDb checks: declaring it on the containers fails -strict with "has groups not defined in parent". So a strand is a matrix cell, and the containers carry no subGroups. Sample class survives as a filterComposite dimension, replacing the facet. configurable on gives each subtrack its own config namespace. Drop the faceted machinery: the metadata table, the color file, the constants feeding them and the gbdbDir argument, 39 lines. The metadata.tsv and colors.json already written under /gbdb are now unreferenced and can be deleted. Put the ENCODE accession in each subtrack longLabel, and add a linked table of them to both description pages. A longLabel cannot carry a link, since printSubtrackTableBody() htmlEncodes it, hence the table. The label wording is shortened to keep the longest at 74 characters. diff --git src/hg/makeDb/trackDb/human/encode4ProCap.html src/hg/makeDb/trackDb/human/encode4ProCap.html index e6831ba0819..8cdb28e0b59 100644 --- src/hg/makeDb/trackDb/human/encode4ProCap.html +++ src/hg/makeDb/trackDb/human/encode4ProCap.html @@ -1,171 +1,183 @@ <h2>Description</h2> <p> Transcription begins when RNA polymerase II starts making an RNA at a transcription start site. A promoter or an enhancer does not use a single start site: polymerase initiates across a spread of nearby bases, on both strands, and which bases are used is set largely by the local DNA sequence. PRO-cap is a nascent RNA run-on assay that captures the 5' end of each new transcript, so each read reports the exact base and strand of one initiation event. Unlike RNA-seq or CAGE, PRO-cap sees unstable RNAs as well as stable ones, which makes initiation at enhancers visible. </p> <p> This track shows PRO-cap signal from six ENCODE 4 experiments, one per cell line, on GRCh38/hg38 only. The predictions a deep learning model makes from sequence alone, trained on this same data, are in the ProCapNet track, available on GRCh38/hg38 and T2T-CHM13/hs1. </p> <h2>Display Conventions and Configuration</h2> <p> -Cell lines are listed in the table on this page, one row each. Use the <b>Sample -class</b> facet to narrow the list, and the <b>Experiment</b> column to open the experiment -on the ENCODE portal. +The matrix on this page has one row per cell line and one column per strand, so a +checkbox turns on one strand of one cell line. Use the <b>Sample class</b> filter +to restrict the matrix to cancer or non-cancer lines. </p> <p> Each track is an overlay of the two strands: plus strand reads are drawn upward and minus strand reads downward. The y axis is the number of initiation events measured at that base, summed over the experiment's replicates, so tracks with deeper sequencing reach higher values. Tracks are colored by cell line: </p> <ul> <li><span style="display:inline-block; background-color:#0072B2; width:18px; height:12px; vertical-align:middle;"></span> <b>A673</b> Ewing sarcoma</li> <li><span style="display:inline-block; background-color:#D55E00; width:18px; height:12px; vertical-align:middle;"></span> <b>Caco-2</b> colorectal adenocarcinoma</li> <li><span style="display:inline-block; background-color:#009E73; width:18px; height:12px; vertical-align:middle;"></span> <b>Calu3</b> lung adenocarcinoma</li> <li><span style="display:inline-block; background-color:#CC79A7; width:18px; height:12px; vertical-align:middle;"></span> <b>HUVEC</b> umbilical vein endothelial cells</li> <li><span style="display:inline-block; background-color:#E69F00; width:18px; height:12px; vertical-align:middle;"></span> <b>K562</b> chronic myelogenous leukemia</li> <li><span style="display:inline-block; background-color:#56B4E9; width:18px; height:12px; vertical-align:middle;"></span> <b>MCF10A</b> non-tumorigenic breast epithelium</li> </ul> +<p> +The six experiments, each linking to its record on the ENCODE portal. +</p> + +<table class="stdTbl"> +<tr><th>Cell line</th><th>Tissue</th><th>Sample class</th><th>ENCODE experiment</th></tr> +<tr><td>A673</td><td>Muscle</td><td>Cancer</td><td><a href="https://www.encodeproject.org/experiments/ENCSR046BCI/" target="_blank">ENCSR046BCI</a></td></tr> +<tr><td>Caco-2</td><td>Colon</td><td>Cancer</td><td><a href="https://www.encodeproject.org/experiments/ENCSR100LIJ/" target="_blank">ENCSR100LIJ</a></td></tr> +<tr><td>Calu3</td><td>Lung</td><td>Cancer</td><td><a href="https://www.encodeproject.org/experiments/ENCSR935RNW/" target="_blank">ENCSR935RNW</a></td></tr> +<tr><td>HUVEC</td><td>Blood vessel</td><td>Non-cancer</td><td><a href="https://www.encodeproject.org/experiments/ENCSR098LLB/" target="_blank">ENCSR098LLB</a></td></tr> +<tr><td>K562</td><td>Blood</td><td>Cancer</td><td><a href="https://www.encodeproject.org/experiments/ENCSR261KBX/" target="_blank">ENCSR261KBX</a></td></tr> +<tr><td>MCF10A</td><td>Breast</td><td>Non-cancer</td><td><a href="https://www.encodeproject.org/experiments/ENCSR799DGV/" target="_blank">ENCSR799DGV</a></td></tr> +</table> + <h2>Methods</h2> <p> PRO-cap, in the CoPRO form of Tome <em>et al.</em>, 2018, runs a nuclear run-on reaction with biotinylated NTPs, captures the biotinylated nascent RNAs, selects for a 5' cap so that only transcripts carrying their original start are kept, and sequences them paired-end. The 5' end of the second read marks the base at which transcription started and its strand gives the strand of initiation. The six experiments were produced by the Yu and Lis labs at Cornell University as part of the ENCODE 4 nascent transcriptome survey described in Shah <em>et al.</em>, 2026, and processed through the ENCODE PRO-cap pipeline. </p> <p> The signal files were downloaded from the <a href="https://www.encodeproject.org" target="_blank">ENCODE portal</a>, taking only the plus and minus strand signal of unique reads belonging to each experiment's default analysis. ENCODE publishes no pooled file, so the per-replicate files were summed at UCSC into one track per cell line and strand, the same merge the ProCapNet models were trained on. Total signal is conserved -exactly by the summing, and minus strand signal is negative as released. The -experiments are ENCSR046BCI, ENCSR100LIJ, ENCSR935RNW, ENCSR098LLB, ENCSR261KBX -and ENCSR799DGV for A673, Caco-2, Calu3, HUVEC, K562 and MCF10A respectively. +exactly by the summing, and minus strand signal is negative as released. </p> <p> The steps are recorded in <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/transcriptionStart.txt" target="_blank">doc/hg38/transcriptionStart.txt</a>, the scripts are in <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/outside/proCapNet" target="_blank">makeDb/outside/proCapNet</a>, including <tt>proCapNetEncodeFiles.tsv</tt>, which records exactly which ENCODE file accessions went into each track, and the track configuration is in <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/trackDb/human/hg38/transcriptionStart.ra" target="_blank">trackDb/human/hg38/transcriptionStart.ra</a>. </p> <h2>Data Access</h2> <p> The bigWig files are on our <a href="http://hgdownload.soe.ucsc.edu/gbdb/hg38/encode4ProCap/" target="_blank">download server</a>, named for the cell line, the ENCODE experiment accession and the strand, for example <tt>K562.ENCSR261KBX.pos.bw</tt> and <tt>K562.ENCSR261KBX.neg.bw</tt>. </p> <p> The data can be explored interactively in table format with the <a href="../cgi-bin/hgTables">Table Browser</a> or the <a href="../cgi-bin/hgIntegrator">Data Integrator</a> and exported from there to spreadsheet or tab-sep tables. From scripts, the data can be accessed through our <a href="https://api.genome.ucsc.edu" target="_blank">API</a>. The API returns one bigWig at a time, so name a single strand of one cell line rather than the container, for example track=<i>encode4ProCap_K562_procap_pos</i>. </p> <p> Individual regions or the whole genome annotation can be obtained using our tool <tt>bigWigToBedGraph</tt>, which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries are on the <a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads" target="_blank">utilities download page</a>. The tool can also be used to obtain features within a given range, e.g. <tt>bigWigToBedGraph http://hgdownload.soe.ucsc.edu/gbdb/hg38/encode4ProCap/K562.ENCSR261KBX.pos.bw -chrom=chr21 -start=0 -end=100000000 stdout</tt> </p> <p> The unmerged per-replicate files can be downloaded from the <a href="https://www.encodeproject.org" target="_blank">ENCODE portal</a> under the experiment accessions listed above. </p> <h2>Credits</h2> <p> PRO-cap data was generated as part of ENCODE by Sagar Shah and the Yu and Lis labs at Cornell University. Thanks to the ENCODE Consortium and the ENCODE production laboratories for making the data available. </p> <h2>References</h2> <p> Shah SR, Chen Y, Leung AK, Navarro PVC, Paramo MI, Gupta J, Gurumurthy A, Fite RF, Weimer AK, Cochran K <em>et al</em>. <a href="https://www.ncbi.nlm.nih.gov/pubmed/41040139" target="_blank"> The nascent transcriptome delineates the regulatory landscape in human health and disease</a>. <em>bioRxiv</em>. 2026 Jun 9;. DOI: <a href="https://doi.org/10.1101/2025.09.24.676871" target="_blank">10.1101/2025.09.24.676871</a>; PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/41040139" target="_blank">41040139</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12485982/" target="_blank">PMC12485982</a> </p> <p> Tome JM, Tippens ND, Lis JT. <a href="https://www.ncbi.nlm.nih.gov/pubmed/30349116" target="_blank"> Single-molecule nascent RNA sequencing identifies regulatory domain architecture at promoters and enhancers</a>. <em>Nat Genet</em>. 2018 Nov;50(11):1533-1541. DOI: <a href="https://doi.org/10.1038/s41588-018-0234-5" target="_blank">10.1038/s41588-018-0234-5</a>; PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/30349116" target="_blank">30349116</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6422046/" target="_blank">PMC6422046</a> </p> <p> Kwak H, Fuda NJ, Core LJ, Lis JT. <a href="https://www.ncbi.nlm.nih.gov/pubmed/23430654" target="_blank"> Precise maps of RNA polymerase reveal how promoters direct initiation and pausing</a>. <em>Science</em>. 2013 Feb 22;339(6122):950-3. 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