---------------------------------------------------------------


mm10.trackDb.html : Differences exist between hgwbeta and hgw2 

(RR fields taken from public MySql server, not individual machine)

12735,12739c12735,12740
< jaspar | This track represents the genome-wide predicted binding 
< jaspar | sites for TF (transcription factor) binding profiles in the 
< jaspar | <a href="https://jaspar.elixir.no/genome-tracks/" target="_blank">JASPAR</a> 
< jaspar | database CORE collection.
< jaspar | </p>
---
> jaspar | This track represents genome-wide predicted binding sites for TF 
> jaspar | (transcription factor) binding profiles in the 
> jaspar | <a href="https://jaspar.genereg.net/about/" target="_blank">JASPAR 
> jaspar | CORE collection</a>. This open-source database contains a curated, non-redundant 
> jaspar | set of binding profiles derived from published collections of experimentally 
> jaspar | defined transcription factor binding sites for eukaryotes.</p>

12825,12851c12826,12833
< jaspar | For each TF binding profile in the JASPAR database CORE collection, genomes were scanned for matches.
< jaspar | </p>
< jaspar | <p>
< jaspar | For the computation of relative scores and p-values, we used PWMScan (Ambrosini et al. 2018). 
< jaspar | We selected TFBS predictions with a PWM relative score &ge; 0.8 and a p-value &lt; 0.05.
< jaspar | P-values were scaled between 0 (corresponding to a p-value of 1) and 1000 (p-value &le; 10<sup>-10</sup>)
< jaspar | for colouring of the genome tracks and to allow for comparison of prediction confidence between 
< jaspar | different profiles.
< jaspar | </p>
< jaspar | <p>
< jaspar | Please refer to the supplementary information of the <a href="https://doi.org/10.1093/nar/gkz1001">JASPAR 2020 manuscript</a> for more details.
< jaspar | </p>
< jaspar | <h3>Brief overview of each release</h3>
< jaspar | <p>
< jaspar | The JASPAR 2026 update expanded the JASPAR CORE collection by 12% (306
< jaspar | added or upgraded profiles), culminating to a set of 2633 non-redundant
< jaspar | TF binding profiles.  Genome sequences were scanned with JASPAR 2026
< jaspar | CORE TF binding profiles for each taxon independently using PWMScan.
< jaspar | TFBS predictions were selected with a PWM relative score &ge; 0.8 and a
< jaspar | p-value &lt; 0.05. P-values were scaled between 0 (corresponding to a
< jaspar | p-value of 1) and 1000 (p-value &le; 10<sup>-10</sup>) for coloring of the genome
< jaspar | tracks and to allow for comparison of prediction confidence between
< jaspar | different profiles. More information on the methods can be found in the
< jaspar | <a href="https://doi.org/10.1093/nar/gkaf1209" target="_blank">JASPAR 2026 
< jaspar | publication</a> or on the
< jaspar | <a href="https://jaspar.elixir.no/" target="_blank">JASPAR website</a>.</p>
< jaspar | 
---
> jaspar | JASPAR 2026 features a deep learning (DL) collection, providing a paradigm shift in modeling 
> jaspar | and characterizing TF-DNA interactions with 1259 BPNet models trained on Homo sapiens ENCODE 
> jaspar | chromatin immunoprecipitation followed by sequencing (ChIP-seq) datasets from 240 TFs and 
> jaspar | interpreted to reveal predictive motif patterns for the models. The motifs associated with 
> jaspar | the same TF were clustered to provide a summary of the binding properties, resulting in 
> jaspar | 240 primary and 113 alternative motif patterns in the DL collection. See the <a 
> jaspar | target="_blank" href="https://pubmed.ncbi.nlm.nih.gov/41325984/">JASPAR 2026 publication</a>
> jaspar | for more information.</p>

12891a12874,12877
> jaspar | <p>
> jaspar | Please refer to the JASPAR 2024, 2022, 2020, and 2018 publications for more 
> jaspar | details (citation below).</p>
> jaspar | 

12894,12896c12880,12881
< jaspar | JASPAR Transcription Factor Binding data includes billions of items.
< jaspar | Because of the data size, the Table Browser does not allow "Genome" as a query region for this
< jaspar | track. Limited regions can be explored interactively with the
---
> jaspar | JASPAR Transcription Factor Binding data includes billions of items. Limited regions can 
> jaspar | be explored interactively with the 

12934,12937c12919,12927
< jaspar |   <li>Binding site predictions for all and individual TF profiles are available for download 
< jaspar |     at <a href="https://mencius.uio.no/JASPAR/JASPAR_genome_browser_tracks/" target="_blank">https://mencius.uio.no/JASPAR/JASPAR_genome_browser_tracks/</a>.</li>
< jaspar |   <li>Code used to create the UCSC tracks is available at <a href="https://github.com/ievarau/JASPAR-UCSC-tracks/tree/master">https://github.com/ievarau/JASPAR-UCSC-tracks/tree/master</a>.</li>
< jaspar |   <li>The underlying JASPAR motif data is available through the JASPAR website at <a href="https://jaspar.elixir.no/" target="_blank">https://jaspar.elixir.no</a>.</li>
---
> jaspar | <li>Binding site predictions for all and individual TF profiles are available 
> jaspar | for download at 
> jaspar | <a href="http://expdata.cmmt.ubc.ca/JASPAR/downloads/UCSC_tracks/"
> jaspar | target="_blank">http://expdata.cmmt.ubc.ca/JASPAR/downloads/UCSC_tracks/</a>.</li>
> jaspar | <li>Code and data used to create the UCSC tracks are available at 
> jaspar | <a href="https://github.com/wassermanlab/JASPAR-UCSC-tracks" target="_blank">
> jaspar | https://github.com/wassermanlab/JASPAR-UCSC-tracks</a>.</li>
> jaspar | <li>The underlying JASPAR motif data is available through the JASPAR website at
> jaspar | <a href="https://jaspar.genereg.net/" target="_blank">https://jaspar.genereg.net/</a>.</li>

12940d12929
< jaspar | 

12943c12932
< jaspar | genomes. The 2026 release is available as a native track on the following genomes, and additionally 
---
> jaspar | genomes. The 20206 release is available as a native track on the following genomes, and additionally 

12945c12934
< jaspar | <a href="../cgi-bin/hgHubConnect#publicHubs">
---
> jaspar | <a href="../cgi-bin/hgHubConnect?hubSearchTerms=jaspar&hgHub_do_search=on">

12955,12956c12944,12945
< jaspar |       <td><a target="_blank"
< jaspar | href="../cgi-bin/hgTrackUi?db=hg38&g=jaspar">hg38</a></td>
---
> jaspar |       <td width="200"><a target="_blank" href="../cgi-bin/hgTrackUi?db=hg19&g=jaspar">hg19</a>, 
> jaspar | <a target="_blank" href="../cgi-bin/hgTrackUi?db=hg38&g=jaspar">hg38</a></td>

12960,12961c12949,12950
< jaspar |       <td><a target="_blank"
< jaspar | href="../cgi-bin/hgTrackUi?db=mm39&g=jaspar">mm39</a></td>
---
> jaspar |       <td><a target="_blank" href="../cgi-bin/hgTrackUi?db=mm10&g=jaspar">mm10</a>, 
> jaspar | <a target="_blank" href="../cgi-bin/hgTrackUi?db=mm39&g=jaspar">mm39</a></td>

12966c12955
< jaspar | href="../cgi-bin/hgTrackUi?db=danRer11&g=jaspar">danRer11</a></td>
---
> jaspar | href="../cgi-bin/hgTracks?db=danRer11&hubUrl=http://expdata.cmmt.ubc.ca/JASPAR/UCSC_tracks/hub.txt">danRer11</a></td>

12971c12960
< jaspar | href="../cgi-bin/hgTrackUi?db=dm6&g=jaspar">dm6</a></td>
---
> jaspar | href="../cgi-bin/hgTracks?db=dm6&hubUrl=http://expdata.cmmt.ubc.ca/JASPAR/UCSC_tracks/hub.txt">dm6</a></td>

12976c12965,12967
< jaspar | href="../cgi-bin/hgTrackUi?db=ce11&g=jaspar">ce11</a></td>
---
> jaspar | href="../cgi-bin/hgTracks?db=ce10&hubUrl=http://expdata.cmmt.ubc.ca/JASPAR/UCSC_tracks/hub.txt">ce10</a>,
> jaspar |       <a target="_blank"
> jaspar | href="../cgi-bin/hgTracks?db=ce11&hubUrl=http://expdata.cmmt.ubc.ca/JASPAR/UCSC_tracks/hub.txt">ce11</a></td>

12981c12972
< jaspar | href="../cgi-bin/hgTrackUi?db=ci3&g=jaspar">ci3</a></td>
---
> jaspar | href="../cgi-bin/hgTracks?db=ci3&hubUrl=http://expdata.cmmt.ubc.ca/JASPAR/UCSC_tracks/hub.txt">ci3</a></td>

12986c12977
< jaspar | href="../cgi-bin/hgTracks?genome=araTha1&hubUrl=https://mencius.uio.no/JASPAR/JASPAR_genome_browser_tracks/current/hub.txt">araTha1</a></td>
---
> jaspar | href="../cgi-bin/hgTracks?hubUrl=http://expdata.cmmt.ubc.ca/JASPAR/UCSC_tracks/hub.txt&genome=araTha1">araTha1</a></td>

12991,12996c12982
< jaspar | href="../cgi-bin/hgTrackUi?db=sacCer3&g=jaspar">sacCer3</a></td>
< jaspar |     </tr>
< jaspar |     <tr>
< jaspar |       <td>Chicken - <em>Gallus gallus</em></td>
< jaspar |       <td><a target="_blank"
< jaspar | href="../cgi-bin/hgTrackUi?db=galGal6&g=jaspar">galGal6</a></td>
---
> jaspar | href="../cgi-bin/hgTracks?db=sacCer3&hubUrl=http://expdata.cmmt.ubc.ca/JASPAR/UCSC_tracks/hub.txt">sacCer3</a></td>

13003,13027c12989,12997
< jaspar | The JASPAR database is a joint effort between several labs (please see the latest JASPAR 
< jaspar | paper, below). Binding site predictions and UCSC tracks were computed by the CBGR team 
< jaspar | at NCMBM using code developed at the Wasserman Lab. For enquiries about the data, 
< jaspar | please contact Anthony Mathelier (
< jaspar | <A HREF="mailto:&#97;&#110;&#116;&#104;&#111;&#110;y.
< jaspar | &#109;&#97;&#116;&#104;e&#108;&#105;&#101;&#114;&#64;&#110;&#99;&#109;b&#109;.
< jaspar | &#117;i&#111;.
< jaspar | &#110;o">
< jaspar | &#97;&#110;&#116;&#104;&#111;&#110;y.
< jaspar | &#109;&#97;&#116;&#104;e&#108;&#105;&#101;&#114;&#64;&#110;&#99;&#109;b&#109;.
< jaspar | &#117;i&#111;.
< jaspar | &#110;o</A>
< jaspar | <!-- above address is anthony.mathelier at ncmbm.uio.no -->
< jaspar | ) or Ieva Rauluseviciute (
< jaspar | <A HREF="mailto:&#105;&#101;&#118;&#97;.
< jaspar | &#114;&#97;&#117;&#108;us&#101;&#118;&#105;&#99;&#105;u&#116;&#101;&#64;&#110;&#99;m&#98;m.
< jaspar | &#117;&#105;&#111;.
< jaspar | &#110;o">
< jaspar | &#105;&#101;&#118;&#97;.
< jaspar | &#114;&#97;&#117;&#108;us&#101;&#118;&#105;&#99;&#105;u&#116;&#101;&#64;&#110;&#99;m&#98;m.
< jaspar | &#117;&#105;&#111;.
< jaspar | &#110;o</A>
< jaspar | <!-- above address is ieva.rauluseviciute at ncmbm.uio.no -->
< jaspar | ).
< jaspar | </p>
---
> jaspar | The JASPAR database is a joint effort between several labs 
> jaspar | (please see the latest JASPAR paper, below). 
> jaspar | Binding site predictions and UCSC tracks were computed by the Wasserman Lab. For 
> jaspar | enquiries about the data please contact Oriol Fornes 
> jaspar | (<A HREF="mailto:&#111;&#114;&#105;&#111;l&#64;&#99;&#109;&#109;&#116;.
> jaspar | u&#98;&#99;.c&#97;">
> jaspar | &#111;&#114;&#105;&#111;l&#64;&#99;&#109;&#109;&#116;.
> jaspar | u&#98;&#99;.c&#97;</A>
> jaspar | <!-- above address is oriol at cmmt.ubc.ca -->).</p>

13030,13035c13000,13006
< jaspar | <p><em><a href="https://mathelierlab.com/">CBGR</a></em><br>
< jaspar | Computational Biology &amp; Gene Regulation<br>
< jaspar | Norwegian Centre for Molecular Biosciences and Medicine (NCMBM)<br>
< jaspar | University of Oslo<br>
< jaspar | Oslo, Norway
< jaspar | </p>
---
> jaspar |   <p><em><a href="http://cisreg.ca/">Wasserman Lab</a></em><br/>
> jaspar |    Centre for Molecular Medicine and Therapeutics<br/>
> jaspar |    BC Children's Hospital Research Institute<br/>
> jaspar |    Department of Medical Genetics<br/>   
> jaspar |    University of British Columbia<br/>
> jaspar |    Vancouver, Canada
> jaspar |   </p>

13037,13043c13008,13017
< jaspar | <blockquote>
< jaspar | <p><em><a href="https://cisreg.info/">Wasserman Lab</a></em><br>
< jaspar | Centre for Molecular Medicine and Therapeutics<br>
< jaspar | BC Children's Hospital Research Institute<br>
< jaspar | Department of Medical Genetics<br>   
< jaspar | University of British Columbia<br>
< jaspar | Vancouver, Canada
---
> jaspar | 
> jaspar | <h2>References</h2>
> jaspar | <p>
> jaspar | Castro-Mondragon JA, Riudavets-Puig R, Rauluseviciute I, Berhanu Lemma R, Turchi L, Blanc-Mathieu R,
> jaspar | Lucas J, Boddie P, Khan A, Manosalva P&#233;rez N <em>et al</em>.
> jaspar | <a href="https://www.ncbi.nlm.nih.gov/pubmed/34850907" target="_blank">
> jaspar | JASPAR 2022: the 9th release of the open-access database of transcription factor binding
> jaspar | profiles</a>.
> jaspar | <em>Nucleic Acids Res</em>. 2021 Nov 30;.
> jaspar | PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/34850907" target="_blank">34850907</a>

13045d13018
< jaspar | </blockquote>

13046a13020,13031
> jaspar | <p>
> jaspar | Fornes O, Castro-Mondragon JA, Khan A, van der Lee R, Zhang X, Richmond PA, 
> jaspar | Modi BP, Correard S, Gheorghe M, Barana&#353;i&#263; D <em>et al</em>.
> jaspar | <a href="https://www.ncbi.nlm.nih.gov/pubmed/31701148" target="_blank">
> jaspar | JASPAR 2020: update of the open-access database of transcription factor 
> jaspar | binding profiles</a>.
> jaspar | <em>Nucleic Acids Res</em>. 2020 Jan 8;48(D1):D87-D92.
> jaspar | PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/31701148" 
> jaspar | target="_blank">31701148</a>; PMC: <a
> jaspar | href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145627/" 
> jaspar | target="_blank">PMC7145627</a>
> jaspar | </p>

13048d13032
< jaspar | <h2>References</h2>

13050,13055c13034,13043
< jaspar | Ovek Baydar D, Rauluseviciute I, Aronsen DR, Blanc-Mathieu R, Bonthuis I, de Beukelaer H, Ferenc K,
< jaspar | Jegou A, Kumar V, Lemma RB <em>et al</em>.
< jaspar | <a href="https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkaf1209" target="_blank">
< jaspar | JASPAR 2026: expansion of transcription factor binding profiles and integration of deep learning models</a>.
< jaspar | <em>Nucleic Acids Res</em>. 2026;
< jaspar | 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>
---
> jaspar | Khan A, Fornes O, Stigliani A, Gheorghe M, Castro-Mondragon JA, van der Lee R, 
> jaspar | Bessy A, Ch&#232;neby J, Kulkarni SR, Tan G <em>et al</em>.
> jaspar | <a href="https://www.ncbi.nlm.nih.gov/pubmed/29140473" target="_blank">
> jaspar | JASPAR 2018: update of the open-access database of transcription factor 
> jaspar | binding profiles and its web framework</a>.
> jaspar | <em>Nucleic Acids Res</em>. 2018 Jan 4;46(D1):D260-D266.
> jaspar | PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/29140473" 
> jaspar | target="_blank">29140473</a>; PMC: <a
> jaspar | href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753243/" 
> jaspar | target="_blank">PMC5753243</a>

13059,13063c13047,13053
< jaspar | Sandelin A, Alkema W, Engstrom P, Wasserman WW, Lenhard B.
< jaspar | <a href="https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkh012" target="_blank">
< jaspar | JASPAR: an open-access database for eukaryotic transcription factor binding profiles</a>.
< jaspar | <em>Nucleic Acids Res</em>. 2004;.
< jaspar | PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14681366" target="_blank">14681366</a>
---
> jaspar | Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, Castro-Mondragon JA, Ferenc K, Kumar V, Lemma
> jaspar | RB, Lucas J, Ch&#232;neby J, Baranasic D <em>et al</em>.
> jaspar | <a href="https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkad1059" target="_blank">
> jaspar | JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding
> jaspar | profiles</a>.
> jaspar | <em>Nucleic Acids Res</em>. 2023 Nov 14;.
> jaspar | PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/37962376" target="_blank">37962376</a>

13065a13056,13065
> jaspar | <p>
> jaspar | Ovek Baydar D, Rauluseviciute I, Aronsen DR, Blanc-Mathieu R, Bonthuis I, de Beukelaer H, Ferenc K,
> jaspar | Jegou A, Kumar V, Lemma RB <em>et al</em>.
> jaspar | <a href="https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkaf1209" target="_blank">
> jaspar | JASPAR 2026: expansion of transcription factor binding profiles and integration of deep learning
> jaspar | models</a>.
> jaspar | <em>Nucleic Acids Res</em>. 2026 Jan 6;54(D1):D184-D193.
> jaspar | PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/41325984" target="_blank">41325984</a>; PMC: <a
> jaspar | href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12807658/" target="_blank">PMC12807658</a>
> jaspar | </p>