59c5f45a1b1d3a94b3b618dc4b307157bd343566 dschmelt Fri Aug 27 13:51:21 2021 -0700 Modifying description page and removing pennantIcon refs #27061 diff --git src/hg/makeDb/trackDb/human/jaspar.html src/hg/makeDb/trackDb/human/jaspar.html index 3a6ed80..fe12ef9 100644 --- src/hg/makeDb/trackDb/human/jaspar.html +++ src/hg/makeDb/trackDb/human/jaspar.html @@ -2,31 +2,30 @@ <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> <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 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> <p> <em>From <a href="../../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;"> @@ -106,63 +105,68 @@ <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).</p> +scanned in parallel using the best software available at the time.</p> <p> -For scanning genomes with the -BioPerl TFBS module, we converted profiles to PWMs and kept matches with a +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 -remaining TFBS predictions were converted to genome tracks and colored according +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 (24). We selected TFBS predictions +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> <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 interacted with through command line utilities. Please be aware that these download files are very large, between 75Gb and 86Gb.</p> <p> -All data is freely available.</p> - -<p> +All data is 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"> 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> <h2>Other Genomes</h2> <p>The JASPAR group provides TFBS predictions for many additional species and @@ -205,37 +209,37 @@ <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 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> +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://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> Fornes O, Castro-Mondragon JA, Khan A, van der Lee R, Zhang X, Richmond PA, Modi BP, Correard S, Gheorghe M, Baranasic D, Santana-Garcia W, Tan G, Cheneby J, Ballester B,