0f951bfc96241a7362d1512ceecf59a02682a839 markd Thu Sep 24 20:40:52 2026 -0700 Description page fixes from a QA pre-pass on the TSS tracks. refs #35528 Encode the non-ASCII character in the Avsec reference on proCapNet.html. getTrackReferences emits raw UTF-8, which the browser does not transcode. Use $db rather than a hardcoded hg38 in the proCapNet download-server link and the bigWigToBedGraph example. One page serves both assemblies, so an hs1 reader was being pointed at hg38 files. Add a Source subsection to proCapNet.html linking the makedoc, the build scripts, the trackDb file and the upstream kundajelab/ProCapNet repository. These links went missing when the Processing at UCSC section was dropped; the prose stays dropped. Drop the cross-links between the two track pages. Track names are prefixed hub_<id>_ on hs1, which is a curated hub, and the id is machine-specific, so a bare-name link cannot work there. Each page now states which assemblies the data is available on instead, naming both GRCh38/hg38 and T2T-CHM13/hs1. Bold the two UI control names on the proCapNet display conventions section. diff --git src/hg/makeDb/trackDb/human/transcriptionStart.html src/hg/makeDb/trackDb/human/transcriptionStart.html index 5506f6625a7..88bf531564e 100644 --- src/hg/makeDb/trackDb/human/transcriptionStart.html +++ src/hg/makeDb/trackDb/human/transcriptionStart.html @@ -1,100 +1,101 @@ <h2>Description</h2> <p> Transcription begins when RNA polymerase II starts making an RNA at a transcription start site (TSS). A gene or a regulatory element does not use a single start site: polymerase initiates across a spread of nearby bases, on both strands, and which bases get used is set largely by the local DNA sequence and by the chromatin state around it. Knowing where transcription starts, and how sharply, matters for reading a promoter, for telling a promoter from an enhancer, and for deciding which of a gene's annotated transcripts is actually made in a given cell. </p> <p> Transcription start site is the common term and the one used here, but it names a position where transcription initiation is the event. Initiation is the more accurate word: polymerase does not start at one fixed point but initiates over a window of bases, at rates that differ base by base, so what these tracks report is the distribution of initiation across a region rather than a single site. </p> <p> No single assay settles where a TSS is. Run-on methods catch the nascent RNA at the moment it is made, cap-based methods read the protected 5' end of a finished transcript, long reads follow a transcript from one end to the other, and sequence models predict initiation without an experiment at all. Each sees a different slice of the same event, and they disagree in informative ways. This collection gathers those lines of evidence in one place so they can be compared at a locus. </p> <p> Tracks currently in the collection: </p> <ul> -<li><a href="hgTrackUi?g=encode4ProCap">PRO-cap</a>: initiation events measured -directly by PRO-cap in six cell lines by ENCODE 4.</li> -<li><a href="hgTrackUi?g=proCapNet">ProCapNet</a>: genome-wide, base-resolution +<li>PRO-cap: initiation events measured +directly by PRO-cap in six cell lines by ENCODE 4. Available on GRCh38/hg38 +only.</li> +<li>ProCapNet: genome-wide, base-resolution predictions of initiation from DNA sequence alone, from six models each trained on one of those cell lines, together with per-base scores showing which bases -each model used.</li> +each model used. The predictions are available on GRCh38/hg38 and +T2T-CHM13/hs1; the per-base scores are available on GRCh38/hg38 only.</li> </ul> <p> Each track has its own description page covering what it measures or predicts, -how it was made, and how to download it. On T2T-CHM13 only the ProCapNet -predictions are available, since the PRO-cap experiments and the contribution -scores were produced against GRCh38. More TSS evidence tracks will be added here -over time. +how it was made, and how to download it. The PRO-cap experiments and the +contribution scores were produced against GRCh38, which is why neither is on +T2T-CHM13. More TSS evidence tracks will be added to this collection over time. </p> <h2>Display Conventions and Configuration</h2> <p> Tracks are grouped by the evidence they carry, with measurements before predictions. Signal tracks that distinguish the two strands draw the plus strand upward and the minus strand downward, so a divergent promoter reads as a pair of peaks straddling the element. </p> <h2>Data Access</h2> <p> Each track listed above has its own description page with details on methods, file locations and how to download and intersect the data. </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. ProCapNet was developed by Kelly Cochran in the Kundaje lab at Stanford University, and the genome-wide predictions and contribution scores were generated in collaboration with the GENCODE consortium. </p> <h2>References</h2> <p> Cochran K, Yin M, Mantripragada A, Schreiber J, Marinov GK, Shah SR, Yu H, Lis JT, Kundaje A. <a href="https://www.ncbi.nlm.nih.gov/pubmed/38853896" target="_blank"> Dissecting the cis-regulatory syntax of transcription initiation with deep learning</a>. <em>bioRxiv</em>. 2024 Nov 21;. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/38853896" target="_blank">38853896</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11160661/" target="_blank">PMC11160661</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. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/23430654" target="_blank">23430654</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3974810/" target="_blank">PMC3974810</a> </p>