29756f1e91ffb40869bee417c95f233c3ceadbff gperez2 Tue Feb 10 16:14:41 2026 -0800 Updating the jaspar track description page, refs #36264 diff --git src/hg/makeDb/trackDb/jaspar.html src/hg/makeDb/trackDb/jaspar.html index 767ffcb4572..8f748dcc015 100644 --- src/hg/makeDb/trackDb/jaspar.html +++ src/hg/makeDb/trackDb/jaspar.html @@ -187,79 +187,83 @@ <li>Binding site predictions for all and individual TF profiles are available for download at <a href="http://expdata.cmmt.ubc.ca/JASPAR/downloads/UCSC_tracks/" target="_blank">http://expdata.cmmt.ubc.ca/JASPAR/downloads/UCSC_tracks/</a>.</li> <li>Code and data used to create the UCSC tracks are available at <a href="https://github.com/wassermanlab/JASPAR-UCSC-tracks" target="_blank"> https://github.com/wassermanlab/JASPAR-UCSC-tracks</a>.</li> <li>The underlying JASPAR motif data is available through the JASPAR website at <a href="https://jaspar.genereg.net/" target="_blank">https://jaspar.genereg.net/</a>.</li> </ul> <h2>Other Genomes</h2> <p>The JASPAR group provides TFBS predictions for many additional species and genomes. The 2026 release is available as a native track on the following genomes, and additionally on mm10 and araTha1 by connection to their -<a href="../cgi-bin/hgHubConnect?hubSearchTerms=jaspar&hgHub_do_search=on"> +<a href="../cgi-bin/hgHubConnect#publicHubs"> Public Hub</a> or by clicking the assembly links below:</p> <table width="458" border="1"> <tbody> <tr> <td><strong>Species</strong></td> <td><strong>Genome assembly versions</strong></td> </tr> <tr> <td width="300">Human - <em>Homo sapiens</em></td> - <td width="200"><a target="_blank" href="../cgi-bin/hgTrackUi?db=hg19&g=jaspar">hg19</a>, -<a target="_blank" href="../cgi-bin/hgTrackUi?db=hg38&g=jaspar">hg38</a></td> + <td><a target="_blank" +href="../cgi-bin/hgTrackUi?db=hg38&g=jaspar">hg38</a></td> </tr> <tr> <td>Mouse - <em>Mus musculus</em></td> - <td><a target="_blank" href="../cgi-bin/hgTrackUi?db=mm10&g=jaspar">mm10</a>, -<a target="_blank" href="../cgi-bin/hgTrackUi?db=mm39&g=jaspar">mm39</a></td> + <td><a target="_blank" +href="../cgi-bin/hgTrackUi?db=mm39&g=jaspar">mm39</a></td> </tr> <tr> <td>Zebrafish - <em>Danio rerio</em></td> <td><a target="_blank" -href="../cgi-bin/hgTracks?db=danRer11&hubUrl=http://expdata.cmmt.ubc.ca/JASPAR/UCSC_tracks/hub.txt">danRer11</a></td> +href="../cgi-bin/hgTrackUi?db=danRer11&g=jaspar">danRer11</a></td> </tr> <tr> <td>Fruitfly - <em>Drosophila melanogaster</em></td> <td><a target="_blank" -href="../cgi-bin/hgTracks?db=dm6&hubUrl=http://expdata.cmmt.ubc.ca/JASPAR/UCSC_tracks/hub.txt">dm6</a></td> +href="../cgi-bin/hgTrackUi?db=dm6&g=jaspar">dm6</a></td> </tr> <tr> <td>Nematode - <em>Caenorhabditis elegans</em></td> <td><a target="_blank" -href="../cgi-bin/hgTracks?db=ce10&hubUrl=http://expdata.cmmt.ubc.ca/JASPAR/UCSC_tracks/hub.txt">ce10</a>, <a target="_blank" -href="../cgi-bin/hgTracks?db=ce11&hubUrl=http://expdata.cmmt.ubc.ca/JASPAR/UCSC_tracks/hub.txt">ce11</a></td> +href="../cgi-bin/hgTrackUi?db=ce11&g=jaspar">ce11</a></td> </tr> <tr> <td>Vase tunicate - <em>Ciona intestinalis</em></td> <td><a target="_blank" -href="../cgi-bin/hgTracks?db=ci3&hubUrl=http://expdata.cmmt.ubc.ca/JASPAR/UCSC_tracks/hub.txt">ci3</a></td> +href="../cgi-bin/hgTrackUi?db=ci3&g=jaspar">ci3</a></td> </tr> <tr> <td>Thale cress - <em>Arabidopsis thaliana</em></td> <td><a target="_blank" -href="../cgi-bin/hgTracks?hubUrl=http://expdata.cmmt.ubc.ca/JASPAR/UCSC_tracks/hub.txt&genome=araTha1">araTha1</a></td> +href="../cgi-bin/hgTracks?genome=araTha1&hubUrl=https://mencius.uio.no/JASPAR/JASPAR_genome_browser_tracks/current/hub.txt">araTha1</a></td> </tr> <tr> <td>Yeast - <em>Saccharomyces cerevisiae</em></td> <td><a target="_blank" -href="../cgi-bin/hgTracks?db=sacCer3&hubUrl=http://expdata.cmmt.ubc.ca/JASPAR/UCSC_tracks/hub.txt">sacCer3</a></td> +href="../cgi-bin/hgTrackUi?db=sacCer3&g=jaspar">sacCer3</a></td> + </tr> + <tr> + <td>Chicken - <em>Gallus gallus</em></td> + <td><a target="_blank" +href="../cgi-bin/hgTrackUi?db=galGal6&g=jaspar">galGal6</a></td> </tr> </tbody> </table> <h2>Credits</h2> <p> The JASPAR database is a joint effort between several labs (please see the latest JASPAR paper, below). Binding site predictions and UCSC tracks were computed by the Wasserman Lab. For enquiries about the data please contact Oriol Fornes (<A HREF="mailto:oriol@cmmt. ubc.ca"> oriol@cmmt. ubc.ca</A> <!-- above address is oriol at cmmt.ubc.ca -->).</p> @@ -299,35 +303,35 @@ </p> <p> Khan A, Fornes O, Stigliani A, Gheorghe M, Castro-Mondragon JA, van der Lee R, Bessy A, Chèneby J, Kulkarni SR, Tan G <em>et al</em>. <a href="https://www.ncbi.nlm.nih.gov/pubmed/29140473" target="_blank"> JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework</a>. <em>Nucleic Acids Res</em>. 2018 Jan 4;46(D1):D260-D266. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/29140473" target="_blank">29140473</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753243/" target="_blank">PMC5753243</a> </p> -<p> -Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, Castro-Mondragon JA, Ferenc K, Kumar V, Lemma -RB, Lucas J, Chèneby J, Baranasic D <em>et al</em>. -<a href="https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkad1059" target="_blank"> -JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding -profiles</a>. -<em>Nucleic Acids Res</em>. 2023 Nov 14;. -PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/37962376" target="_blank">37962376</a> -</p> - <p> Ovek Baydar D, Rauluseviciute I, Aronsen DR, Blanc-Mathieu R, Bonthuis I, de Beukelaer H, Ferenc K, Jegou A, Kumar V, Lemma RB <em>et al</em>. <a href="https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkaf1209" target="_blank"> JASPAR 2026: expansion of transcription factor binding profiles and integration of deep learning models</a>. <em>Nucleic Acids Res</em>. 2026 Jan 6;54(D1):D184-D193. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/41325984" target="_blank">41325984</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12807658/" target="_blank">PMC12807658</a> </p> + +<p> +Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, Castro-Mondragon JA, Ferenc K, Kumar V, Lemma +RB, Lucas J, Chèneby J, Baranasic D <em>et al</em>. +<a href="https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkad1059" target="_blank"> +JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding +profiles</a>. +<em>Nucleic Acids Res</em>. 2023 Nov 14;. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/37962376" target="_blank">37962376</a> +</p>