21fc0d18891023f8b0fd71d503b9e04c36ea98bb dschmelt Thu Sep 2 11:11:48 2021 -0700 Code review phrasing fix refs #27061 diff --git src/hg/makeDb/trackDb/human/jaspar.html src/hg/makeDb/trackDb/human/jaspar.html index 44d3eda..330e0fd 100644 --- src/hg/makeDb/trackDb/human/jaspar.html +++ src/hg/makeDb/trackDb/human/jaspar.html @@ -80,69 +80,66 @@ <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 +(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> 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 +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 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. +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"> 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 @@ -205,29 +202,39 @@ 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, - Parcy F, Sandelin A, Lenhard B, Wasserman WW, Mathelier A. -<strong>JASPAR 2020: update of the open-access database of transcription factor binding -profiles.</strong> <em>Nucleic Acids Res.</em> 2020 . -<a href="https://pubmed.ncbi.nlm.nih.gov/31701148/" target="_blank">PMID 31701148</a></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, Cheneby J, Kulkarni SR, Tan G, Baranasic D, Arenillas DJ, Sandelin A, -Vandepoele K, Lenhard B, Ballester B, Wasserman WW, Parcy F, Mathelier A. -<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> +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>