19870454d7c3d8f29a5800477bcaa36babee5a98 dschmelt Tue Nov 2 17:10:33 2021 -0700 Finishing Development for jaspar update refs #28322 diff --git src/hg/makeDb/trackDb/mouse/jaspar.html src/hg/makeDb/trackDb/mouse/jaspar.html new file mode 100644 index 0000000..d12a69c --- /dev/null +++ src/hg/makeDb/trackDb/mouse/jaspar.html @@ -0,0 +1,224 @@ +<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 only shows predicted binding sites with scores of 400 or greater. +This 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> +JASPAR contains transcription factor binding sites +with additional transcription factor profiles. 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. More information on +the methods can be found in their publications or on the +<a href="https://jaspar.genereg.net/" target="_blank">JASPAR website</a>.</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. +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></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, 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>