73b463410df5d0e73fa068c2eb66df33cfceb6ee dschmelt Fri Aug 20 15:57:37 2021 -0700 Fixing makeDoc location as requested and short html edit refs #27061 diff --git src/hg/makeDb/trackDb/human/jaspar.html src/hg/makeDb/trackDb/human/jaspar.html index f77d7f5..0764aff 100644 --- src/hg/makeDb/trackDb/human/jaspar.html +++ src/hg/makeDb/trackDb/human/jaspar.html @@ -1,165 +1,165 @@ <h2>Description</h2> <p>This UCSC Genome Browser track represents genome-wide predicted binding sites for TF (transcription factor) binding profiles in the <a href="http://jaspar.genereg.net/genome-tracks/" target="_blank">JASPAR</a> database CORE collection.</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 by adjusting the track settings.</p> <p><em>From <a href="https://genome.ucsc.edu/FAQ/FAQformat.html#format1">https://genome.ucsc.edu/FAQ/FAQformat.html#format1</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 cellspacing="0" cellpadding="0"> <col width="87" /> <col width="87" /> <tr> <td width="107"><div align="center"><strong>Track score</strong></div></td> <td width="107"><div align="center"><strong>p-value</strong></div></td> </tr> <tr> <td align="right"><div align="center">0</div></td> <td><div align="center">1</div></td> </tr> <tr> <td align="right"><div align="center">100</div></td> <td><div align="center">0.1</div></td> </tr> <tr> <td align="right"><div align="center">131</div></td> <td><div align="center">0.049</div></td> </tr> <tr> <td align="right"><div align="center">200</div></td> <td><div align="center">10<sup>-2</sup></div></td> </tr> <tr> <td align="right"><div align="center">300</div></td> <td><div align="center">10<sup>-3</sup></div></td> </tr> <tr> <td align="right"><div align="center">400</div></td> <td><div align="center">10<sup>-4</sup></div></td> </tr> <tr> <td align="right"><div align="center">500</div></td> <td><div align="center">10<sup>-5</sup></div></td> </tr> <tr> <td align="right"><div align="center">600</div></td> <td><div align="center">10<sup>-6</sup></div></td> </tr> <tr> <td align="right"><div align="center">700</div></td> <td><div align="center">10<sup>-7</sup></div></td> </tr> <tr> <td align="right"><div align="center">800</div></td> <td><div align="center">10<sup>-8</sup></div></td> </tr> <tr> <td align="right"><div align="center">900</div></td> <td><div align="center">10<sup>-9</sup></div></td> </tr> <tr> <td align="right"><div align="center">1000</div></td> <td><div align="center">≤ 10<sup>-10</sup></div></td> </tr> </table> <h2>Methods</h2> <p>For each TF binding profile in the JASPAR CORE collection, genomes were scanned in parallel using 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 et al. 2009). For scanning genomes with the BioPerl TFBS module, we converted profiles to PWMs and kept matches 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 converted to genome tracks and colored according to their FIMO p-value to allow for comparison of prediction confidence between different profiles.</p> <p>Please refer to the JASPAR 2018 manuscript for more details (citation below).</p> <h2>Data Access</h2> <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/2018/" target="_blank">http://expdata.cmmt.ubc.ca/JASPAR/downloads/UCSC_tracks/2018/</a>.</li> <li>Code and data used to create the UCSC tracks are available at <a href="https://github.com/wassermanlab/JASPAR-UCSC-tracks">https://github.com/wassermanlab/JASPAR-UCSC-tracks</a>.</li> <li>The underlying JASPAR motif data is available through the JASPAR website at <a href="http://jaspar.genereg.net" target="_blank">http://jaspar.genereg.net</a>.</li> </ul> <p> All data is freely available.</p> <h2>Genomes</h2> -<p>The JASPAR group provides TFBS predictions for many additional species and genomes in their Public Hub:</p> +<p>The JASPAR group provides TFBS predictions for many additional species and genomes in their <a href="../cgi-bin/hgHubConnect?hubSearchTerms=jaspar&hgHub_do_search=on">Public Hub</a>:</p> <table width="458" border="1"> <tbody> <tr> <td><strong>Species</strong></td> <td><strong>Genome assembly versions</strong></td> </tr> <tr> <td width="200">Human</td> <td width="200">hg19, hg38</td> </tr> <tr> <td><em>Danio rerio</em></td> <td>danRer10</td> </tr> <tr> <td><em>Drosophila melanogaster</em></td> <td>dm6</td> </tr> <tr> <td><em>Caenorhabditis elegans</em></td> <td>ce10</td> </tr> <tr> <td><em>Arabidopsis thaliana</em></td> <td>araTha1</td> </tr> <tr> <td><em>Saccharomyces cerevisiae</em></td> <td>sacCer3</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 and are maintained by David Arenillas (<a href="mailto:dave@cmmt.ubc.ca" target="_blank">dave@cmmt.ubc.ca</a>). For enquiries about the data please contact Oriol Fornes (<a href="mailto:oriol@cmmt.ubc.ca" target="_blank">oriol@cmmt.ubc.ca</a>) and Robin van der Lee (<a href="mailto:rvdlee@cmmt.ubc.ca" target="_blank">rvdlee@cmmt.ubc.ca</a>). </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> A Khan, O Fornes, A Stigliani, A Bessy, M Gheorghe, R van der Lee, J A Castro-Mondragon, J Cheneby, S R Kulkarni, G Tan, D Baranasic, D J Arenillas, A Sandelin, K Vandepoele, B Lenhard, B Ballester, W W Wasserman, F Parcy, A Mathelier. <strong>JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework</strong>. <em>Nucleic Acids Research</em>. 2018. <a href="https://www.ncbi.nlm.nih.gov/pubmed/29140473">PMID 29140473</a></p>