28d217636eb69c134a1478eaef916ba3cbfdc7b9 gperez2 Tue Mar 5 13:32:49 2024 -0800 Announcing the release of the JASPAR 2024 track, refs #31973 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index c58aaf9..31448d9 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -51,30 +51,90 @@ </div> <p>You can sign-up to get these announcements via our <a target=_blank href="https://groups.google.com/a/soe.ucsc.edu/g/genome-announce?hl=en">Genome-announce</a> email list. We send around one short announcement email every two weeks.</p> <p>Smaller software changes are not announced here. A summary of the three-weekly release changes can be <a target=_blank href="https://genecats.gi.ucsc.edu/builds/versions.html">here</a>. For the full list of our daily code changes head to <a href="https://github.com/ucscGenomeBrowser/kent/commits/master" target=_blank>our GitHub page</a>.</p> <!-- ============= 2024 archived news ============= --> <a name="2024"></a> +<a name="030524"></a> +<h2>Mar. 05, 2024 New JASPAR tracks: Human (hg19/hg38) - Mouse (mm10/mm39)</h2> +<p> +We are excited to announce the new JASPAR 2024 tracks for human +(<a href="/cgi-bin/hgTrackUi?db=hg19&g=jaspar">GRCh37/hg19</a> and +<a href="/cgi-bin/hgTrackUi?db=hg38&g=jaspar">GRCh38/hg38</a>) and +mouse (<a href="/cgi-bin/hgTrackUi?db=mm39&g=jaspar">GRCm39/mm39</a> and +<a href="/cgi-bin/hgTrackUi?db=mm10&g=jaspar">GRCm38/mm10</a>). These tracks represent genome-wide +predicted binding sites for transcription factors with binding profiles in the +<a href="https://jaspar.genereg.net/about/" target="_blank">JASPAR CORE collection</a>. JASPAR CORE +is an open-source database containing a curated, non-redundant set of binding profiles derived from +collections of experimentally defined transcription factor binding profiles. The JASPAR 2024 update +expanded the JASPAR CORE collection by 20% (329 added and 72 upgraded profiles). JASPAR continues +to uphold its core principles (i) providing high-quality TF binding profiles, (ii) fostering open +access, and (iii) ensuring ease of use, which has been useful for the scientific community in +studying gene transcription regulation.</p> +<p> +The JASPAR database is a joint effort between several labs (please see the latest +<a href="https://pubmed.ncbi.nlm.nih.gov/37962376/" target="_blank">JASPAR paper</a>). +Binding site predictions and UCSC tracks were computed by the +<a href="https://mathelierlab.com/" +target="_blank">Computational Biology & Gene Regulation group</a>. We would like to thank Jairo +Navarro and Gerardo Perez at UCSC for building and testing these tracks.</p> + +<a name="030124"></a> +<h2>Mar. 01, 2024 AbSplice Prediction Scores for hg38</h2> +<p> +We are happy to announce the release of the +<a href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=abSplice" target="_blank">AbSplice scores</a> +track for the human genome, GRCh38/hg38. AbSplice is a method that predicts aberrant splicing across +human tissues, as described in <a href="https://doi.org/10.1038/s41588-023-01373-3" +target="_blank">Wagner, Çelik et al., 2023</a>. This track displays precomputed AbSplice +scores for all possible single-nucleotide variants genome-wide. The scores represent the probability +that a given variant causes aberrant splicing in a given tissue.</p> +<p> +Aberrant splicing is a major cause of genetic disorders but its direct detection in transcriptomes +is limited to clinically accessible tissues such as skin or body fluids. Çelik et al. +generated an aberrant splicing benchmark dataset, spanning over 8.8 million rare variants in 49 +human tissues from the Genotype-Tissue Expression (GTEx) dataset. The AbSplice score is a +probability estimate of how likely aberrant splicing of some sort takes place in a given tissue. +The authors <a href="https://github.com/gagneurlab/absplice?tab=readme-ov-file#output" +target="_blank">suggest</a> three cutoffs which are represented by color in the track.</p> + +<ul> + <li><b><font color="#FF0000">High (red)</font></b> - <b> + An AbSplice score over 0.2</b> indicates a high likelihood of aberrant splicing in at least one + tissue.</li> + <li><b><font color="#FF8000">Medium (orange)</font></b> - <b> + A score between 0.05 and 0.2 </b> indicates a medium likelihood.</li> + <li><b><font color="#0000FF">Low (blue)</font></b> - <b> + A score between 0.01 and 0.05 </b> indicates a low likelihood.</li> + <li><b>Scores below 0.01 are not displayed.</b></li> +</ul> + +<p> +We would like to thank Wagner, Çelik et al., 2023 for generating and making the data publicly +available. We would also like to thank Jeltje van Baren and Jairo Navarro for the creation and +release of these tracks. +</p> + <a name="030124"></a> <h2>Mar. 01, 2024 AbSplice Prediction Scores for hg38</h2> <p> We are happy to announce the release of the <a href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=abSplice" target="_blank">AbSplice scores</a> track for the human genome, GRCh38/hg38. AbSplice is a method that predicts aberrant splicing across human tissues, as described in <a href="https://doi.org/10.1038/s41588-023-01373-3" target="_blank">Wagner, Çelik et al., 2023</a>. This track displays precomputed AbSplice scores for all possible single-nucleotide variants genome-wide. The scores represent the probability that a given variant causes aberrant splicing in a given tissue.</p> <p> Aberrant splicing is a major cause of genetic disorders but its direct detection in transcriptomes is limited to clinically accessible tissues such as skin or body fluids. Çelik et al. generated an aberrant splicing benchmark dataset, spanning over 8.8 million rare variants in 49 human tissues from the Genotype-Tissue Expression (GTEx) dataset. The AbSplice score is a