8f0fb6c4a07a0eff3650e49b3a7ad2808f644bc7 dschmelt Fri Aug 27 17:40:45 2021 -0700 Format and text changes for CR refs #28027 diff --git src/hg/makeDb/trackDb/human/jaspar.html src/hg/makeDb/trackDb/human/jaspar.html index fe12ef9..44d3eda 100644 --- src/hg/makeDb/trackDb/human/jaspar.html +++ src/hg/makeDb/trackDb/human/jaspar.html @@ -1,43 +1,43 @@ <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 -p-value ≤ 10<sup>-10</sup>). Thus, the darker the shade, the lower (better) the p-value.</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. Multi-select filters allow viewing of +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 in to see detail.</p> +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">https://genome.ucsc.edu/FAQ/FAQformat.html#format1</a>: +<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> @@ -45,84 +45,60 @@ <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> +<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> For each TF binding profile in the JASPAR CORE collection, genomes were scanned in parallel using the best software available at the time.</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 et al. 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