e00c4ac98aed323e5dba0241250e4ee16369b573 jnavarr5 Mon Jun 3 13:58:55 2024 -0700 Combining all JASPAR tracks to use the same trackDb statement so we can setup automatic updates, refs #32537 diff --git src/hg/makeDb/trackDb/human/jaspar.html src/hg/makeDb/trackDb/human/jaspar.html deleted file mode 100644 index c430c75..0000000 --- src/hg/makeDb/trackDb/human/jaspar.html +++ /dev/null @@ -1,312 +0,0 @@ -<h2>Description</h2> -<p> -This track represents genome-wide predicted binding sites for TF -(transcription factor) binding profiles in the -<a href="https://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 -p-value ≤ 10<sup>-10</sup>). Thus, the darker the shade, the -lower (better) the p-value.</p> - -<p> -The default view shows only predicted binding sites with scores of 400 or greater but -can be adjusted in the track settings. Multi-select filters allow viewing of -particular transcription factors. At window sizes of greater than -10,000 base pairs, this track turns to density graph mode. -Zoom to a smaller region and click into an item to see more detail.</p> - -<p> -<em>From <a href="../../FAQ/FAQformat.html#format1">BED format documentation</a>: - </em> -<table style="box-sizing: border-box; border-collapse: collapse; border-spacing: 0px; border: 2px solid gray; margin-top: 10px; margin-left: 15px; font-size: 13px; color: rgb(0, 0, 0); font-family: 'Helvetica Neue', Helvetica, Arial, sans-serif; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: left; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration-style: initial; text-decoration-color: initial;"> - <tbody style="box-sizing: border-box;"> - <tr style="box-sizing: border-box;"> - <td style="box-sizing: border-box; padding: 1px 15px; text-align: left; border-bottom: 1px solid rgb(221, 221, 221);">shade</td> - <td style="box-sizing: border-box; padding: 1px 15px; text-align: left; border-bottom: 1px solid rgb(221, 221, 221); background-color: rgb(226, 226, 226);"> </td> - <td style="box-sizing: border-box; padding: 1px 15px; text-align: left; border-bottom: 1px solid rgb(221, 221, 221); background-color: rgb(198, 198, 198);"> </td> - <td style="box-sizing: border-box; padding: 1px 15px; text-align: left; border-bottom: 1px solid rgb(221, 221, 221); background-color: rgb(170, 170, 170);"> </td> - <td style="box-sizing: border-box; padding: 1px 15px; text-align: left; border-bottom: 1px solid rgb(221, 221, 221); background-color: rgb(141, 141, 141);"> </td> - <td style="box-sizing: border-box; padding: 1px 15px; text-align: left; border-bottom: 1px solid rgb(221, 221, 221); background-color: rgb(113, 113, 113);"> </td> - <td style="box-sizing: border-box; padding: 1px 15px; text-align: left; border-bottom: 1px solid rgb(221, 221, 221); background-color: rgb(85, 85, 85);"> </td> - <td style="box-sizing: border-box; padding: 1px 15px; text-align: left; border-bottom: 1px solid rgb(221, 221, 221); background-color: rgb(56, 56, 56);"> </td> - <td style="box-sizing: border-box; padding: 1px 15px; text-align: left; border-bottom: 1px solid rgb(221, 221, 221); background-color: rgb(28, 28, 28);"> </td> - <td style="box-sizing: border-box; padding: 1px 15px; text-align: left; border-bottom: 1px solid rgb(221, 221, 221); background-color: rgb(0, 0, 0);"> </td> - </tr> - <tr style="box-sizing: border-box;"> - <td style="box-sizing: border-box; padding: 1px 15px; text-align: left; border-bottom: 1px solid rgb(221, 221, 221);">score in range</td> - <td style="box-sizing: border-box; padding: 1px 15px; text-align: left; border-bottom: 1px solid rgb(221, 221, 221);">≤ 166</td> - <td style="box-sizing: border-box; padding: 1px 15px; text-align: left; border-bottom: 1px solid rgb(221, 221, 221);">167-277</td> - <td style="box-sizing: border-box; padding: 1px 15px; text-align: left; border-bottom: 1px solid rgb(221, 221, 221);">278-388</td> - <td style="box-sizing: border-box; padding: 1px 15px; text-align: left; border-bottom: 1px solid rgb(221, 221, 221);">389-499</td> - <td style="box-sizing: border-box; padding: 1px 15px; text-align: left; border-bottom: 1px solid rgb(221, 221, 221);">500-611</td> - <td style="box-sizing: border-box; padding: 1px 15px; text-align: left; border-bottom: 1px solid rgb(221, 221, 221);">612-722</td> - <td style="box-sizing: border-box; padding: 1px 15px; text-align: left; border-bottom: 1px solid rgb(221, 221, 221);">723-833</td> - <td style="box-sizing: border-box; padding: 1px 15px; text-align: left; border-bottom: 1px solid rgb(221, 221, 221);">834-944</td> - <td style="box-sizing: border-box; padding: 1px 15px; text-align: left; border-bottom: 1px solid rgb(221, 221, 221);">≥ 945</td> - </tr> - </tbody> -</table> - -<p><em>Conversion table:</em></p> -<table border="2" style="padding: 10px; border: 1px solid black; border-collapse: collapse;"> - <tr> - <td style="padding:10px"><strong>Item score</strong></td> - <td style="padding:10px">0</td> - <td style="padding:10px">100</td> - <td style="padding:10px">131</td> - <td style="padding:10px">200</td> - <td style="padding:10px">300</td> - <td style="padding:10px">400</td> - <td style="padding:10px">500</td> - <td style="padding:10px">600</td> - <td style="padding:10px">700</td> - <td style="padding:10px">800</td> - <td style="padding:10px">900</td> - <td style="padding:10px">1000</td> - </tr> - <tr> - <td style="padding:10px"><strong>p-value</strong></td> - <td style="padding:10px">1</td> - <td style="padding:10px">0.1</td> - <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> -The JASPAR 2024 update expanded the JASPAR CORE collection by 20% (329 added and 72 upgraded -profiles). The new profiles were introduced after manual curation, in which 26 629 TF binding -motifs were curated and obtained as PFMs or discovered from ChIP-seq/-exo or DAP-seq data. 2500 -profiles from JASPAR 2022 were revised to either promote them to the CORE collection, update the -associated metadata, or remove them because of validation inconsistencies or poor quality. The -JASPAR database stores and focuses mostly on PFMs as the model of choice for TF-DNA interactions. -More information on the methods can be found in the -<a href="https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkad1059" target="_blank"> -JASPAR 2024 publication</a> or on the -<a href="https://jaspar.genereg.net/" target="_blank">JASPAR website</a>.</p> - -<p> -JASPAR 2022 contains updated transcription factor binding sites -with additional transcription factor profiles. More information on the methods can be found in the -<a href="https://www.ncbi.nlm.nih.gov/pubmed/34850907" target="_blank"> -JASPAR 2022 publication</a> -JASPAR 2022 publication or on the -<a href="https://jaspar.genereg.net/" target="_blank">JASPAR website</a>.</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 -coloring 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> -Please refer to the JASPAR 2024, 2022, 2020, and 2018 publications for more -details (citation below).</p> - -<h2>Data Access</h2> -<p> -JASPAR Transcription Factor Binding data includes billions of items. Limited regions 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>, although positional -queries that are too big can lead to timing out. This results in a black page -or truncated output. In this case, you may try reducing the chromosomal query to -a smaller window.</p> -<p> -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/$db/jaspar">Genome Browser's download server</a> -as a bigBed file. This compressed binary format can be remotely queried through -command line utilities. Please note that some of the download files can be quite large.</p> -<p> -The utilities for working with bigBed-formatted binary files can be downloaded -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads" - target=_blank>here</a>. -Run a utility with no arguments to see a brief description of the utility and its options. -<ul> - <li><b>bigBedInfo</b> provides summary statistics about a bigBed file including the number of - items in the file. With the <b>-as</b> option, the output includes an - autoSql - definition of data columns, useful for interpreting the column values.</li> - <li><b>bigBedToBed</b> converts the binary bigBed data to tab-separated text. - Output can be restricted to a particular region by using the -chrom, -start - and -end options.</li> -</ul> -</p> - -<h4>Example: retrieve all JASPAR items in chr1:200001-200400</h4> - -<pre><tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/$db/jaspar/JASPAR2024.bb -chrom=chr1 -start=200000 -end=200400 stdout</tt></pre> - -<p> -All data are freely available. -Additional resources are available directly from the JASPAR group:</p> -<ul> -<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, 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> - </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> - </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" -href="../cgi-bin/hgTracks?db=dm6&hubUrl=http://expdata.cmmt.ubc.ca/JASPAR/UCSC_tracks/hub.txt">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> - </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> - </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> - </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> - </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> - -<blockquote> - <p><em><a href="http://cisreg.ca/">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 <em>et al</em>. -<a href="https://www.ncbi.nlm.nih.gov/pubmed/34850907" target="_blank"> -JASPAR 2022: the 9th release of the open-access database of transcription factor binding -profiles</a>. -<em>Nucleic Acids Res</em>. 2021 Nov 30;. -PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/34850907" target="_blank">34850907</a> -</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>. -<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>