f9c9ff4d1f24831e1957d6cbf4214072abfb4001 dschmelt Tue Nov 2 11:07:02 2021 -0700 staging jaspar 2022 track and mouse tracks refs #28322 diff --git src/hg/makeDb/trackDb/human/jaspar.html src/hg/makeDb/trackDb/human/jaspar.html index dfbfda7..5318746 100644 --- src/hg/makeDb/trackDb/human/jaspar.html +++ src/hg/makeDb/trackDb/human/jaspar.html @@ -1,16 +1,15 @@ - <h2>Description</h2> <p> This track represents genome-wide predicted binding sites for TF (transcription factor) binding profiles in the <a href="http://jaspar.genereg.net/about/" target="_blank">JASPAR CORE collection</a>. This open-source database contains a curated, non-redundant set of binding profiles derived from published collections of experimentally defined transcription factor binding sites for eukaryotes.</p> <h2>Display Conventions and Configuration</h2> <p> Shaded boxes represent predicted binding sites for each of the TF profiles in the JASPAR CORE collection. The shading of the boxes indicates the p-value of the profile's match to that position (scaled between 0-1000 scores, where 0 corresponds to a p-value of 1 and 1000 to a @@ -80,50 +79,57 @@ <td style="padding:10px">0.049</td> <td style="padding:10px">10<sup>-2</sup></td> <td style="padding:10px">10<sup>-3</sup></td> <td style="padding:10px">10<sup>-4</sup></td> <td style="padding:10px">10<sup>-5</sup></td> <td style="padding:10px">10<sup>-6</sup></td> <td style="padding:10px">10<sup>-7</sup></td> <td style="padding:10px">10<sup>-8</sup></td> <td style="padding:10px">10<sup>-9</sup></td> <td style="padding:10px">≤ 10<sup>-10</sup></td> </tr> </table> <h2>Methods</h2> <p> +JASPAR 2022 contains updates transcription factor binding sites +with additional transcription factor profiles. More information on +the methods can be found in the upcoming publication.</p> + +<p> +JASPAR 2020 scanned DNA sequences with JASPAR CORE TF-binding profiles +for each taxa independently using PWMScan. TFBS predictions were selected with +a PWM relative score ≥ 0.8 and a p-value < 0.05. P-values were scaled +between 0 (corresponding to a p-value of 1) and 1000 (p-value ≤ 10<sup>-10</sup>) for +colouring of the genome tracks and to allow for comparison of prediction +confidence between different profiles.</p> + +<p> JASPAR 2018 used the TFBS Perl module (Lenhard and Wasserman 2002) and FIMO (Grant, Bailey, and Noble 2011), as distributed within the MEME suite (version 4.11.2) (Bailey <em>et al.</em> 2009). For scanning genomes with the BioPerl TFBS module, profiles were converted to PWMs and matches were kept with a relative score ≥ 0.8. For the FIMO scan, profiles were reformatted to MEME motifs and matches with a p-value < 0.05 were kept. TFBS predictions that were not consistent between the two methods (TFBS Perl module and FIMO) were removed. The remaining TFBS predictions were colored according to their FIMO p-value to allow for comparison of prediction confidence between different profiles.</p> -<p> -For JASPAR 2020, DNA sequences were scanned with JASPAR CORE TF-binding profiles -for each taxa independently using PWMScan. TFBS predictions were selected with -a PWM relative score ≥ 0.8 and a p-value < 0.05. P-values were scaled -between 0 (corresponding to a p-value of 1) and 1000 (p-value ≤ 10<sup>-10</sup>) for -colouring of the genome tracks and to allow for comparison of prediction -confidence between different profiles.</p> <p> -Please refer to the JASPAR 2020 and 2018 publication for more details (citation below).</p> +Please refer to the JASPAR 2022, 2020, and 2018 publications for more +details (citation below).</p> <h2>Data Access</h2> <p> JASPAR Transcription Factor Binding data can be explored interactively with the <a href="../cgi-bin/hgTables">Table Browser</a> and cross-referenced with <a href="../cgi-bin/hgIntegrator">Data Integrator</a>. For programmatic access, the track can be accessed using the Genome Browser's <a href="../../goldenPath/help/api.html">REST API</a>. JASPAR annotations can be downloaded from the <a href="http://hgdownload.soe.ucsc.edu/gbdb/$db/jaspar">Genome Browser's download server</a> as a bigBed file. This compressed binary format can be remotely queried through command line utilities. Please note that some of the download files can be quite large.</p> <p> All data are freely available. @@ -141,31 +147,32 @@ </ul> <h2>Other Genomes</h2> <p>The JASPAR group provides TFBS predictions for many additional species and genomes, accessible by connection to their <a href="../cgi-bin/hgHubConnect?hubSearchTerms=jaspar&hgHub_do_search=on"> 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 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> </tr> <tr> <td>Mouse - <em>Mus musculus</em></td> <td><a target="_blank" href="../cgi-bin/hgTracks?db=mm10&hubUrl=http://expdata.cmmt.ubc.ca/JASPAR/UCSC_tracks/hub.txt"> mm10</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> </tr> <tr> <td>Fruitfly - <em>Drosophila melanogaster</em></td> <td><a target="_blank" @@ -201,30 +208,39 @@ ubc.ca</A> <!-- above address is oriol at cmmt.ubc.ca -->).</p> <blockquote> <p><em><a href="http://www.cmmt.ubc.ca/wasserman-lab/">Wasserman Lab</a></em><br/> Centre for Molecular Medicine and Therapeutics<br/> BC Children's Hospital Research Institute<br/> Department of Medical Genetics<br/> University of British Columbia<br/> Vancouver, Canada </p> </blockquote> <h2>References</h2> <p> +Castro-Mondragon JA, Riudavets-Puig R, Rauluseviciute I, Berhanu Lemma R, Turchi L, +Blanc-Mathieu R, Lucas J, Boddie P, Khan A, Manosalva Pérez N, Fornes O, Leung TY, +Aguirre A, Hammal F, Schmelter D, Baranasic D, Ballester B, Sandelin A, Lenhard B, +Vandepoele K, Wasserman WW, Parcy F, and Mathelier A. <b>JASPAR 2022: the 9th +release of the open-access database of transcription factor binding profiles</b> +<em>Nucleic Acids Res</em>. Pending Publication. +</p> + +<p> Fornes O, Castro-Mondragon JA, Khan A, van der Lee R, Zhang X, Richmond PA, Modi BP, Correard S, Gheorghe M, Baranašić D <em>et al</em>. <a href="https://www.ncbi.nlm.nih.gov/pubmed/31701148" target="_blank"> JASPAR 2020: update of the open-access database of transcription factor binding profiles</a>. <em>Nucleic Acids Res</em>. 2020 Jan 8;48(D1):D87-D92. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/31701148" target="_blank">31701148</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145627/" target="_blank">PMC7145627</a> </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>.