b3026b69caa0f44bf3824cc339b012304aef4b41 lrnassar Thu Feb 26 04:56:29 2026 -0800 Feedback from CR, mostly fixing grammar/punctuation and encoding to HTML, refs #37151 diff --git src/hg/makeDb/trackDb/jaspar.html src/hg/makeDb/trackDb/jaspar.html index 9c1bc3ab837..0394fe321c6 100644 --- src/hg/makeDb/trackDb/jaspar.html +++ src/hg/makeDb/trackDb/jaspar.html @@ -82,47 +82,47 @@ <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 database CORE collection, genomes were scanned for matches. </p> <p> For the computation of relative scores and p-values, we used PWMScan (Ambrosini et al. 2018). -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 ≤ 10-10) +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 supplementary information of the <a href="https://doi.org/10.1093/nar/gkz1001">JASPAR 2020 manuscript</a> for more details. </p> <h3>Brief overview of each release</h3> <p> The JASPAR 2026 update expanded the JASPAR CORE collection by 12% (306 added or upgraded profiles), culminating to a set of 2633 non-redundant TF binding profiles. Genome sequences were scanned with JASPAR 2026 CORE TF binding profiles for each taxon independently using PWMScan. -TFBS predictions were selected with a PWM relative score ≥ 0.8 and a +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 ≤ 10⁻¹⁰) for coloring of the genome +p-value of 1) and 1000 (p-value ≤ 10<sup>-10</sup>) for coloring of the genome tracks and to allow for comparison of prediction confidence between different profiles. More information on the methods can be found in the <a href="https://doi.org/10.1093/nar/gkaf1209" target="_blank">JASPAR 2026 publication</a> or on the <a href="https://jaspar.elixir.no/" target="_blank">JASPAR website</a>.</p> <p> The JASPAR 2024 update expanded the JASPAR CORE collection by 20% (329 added and 72 upgraded profiles). The new profiles were introduced after manual curation, in which 26 629 TF binding motifs were curated and obtained as PFMs or discovered from ChIP-seq/-exo or DAP-seq data. 2500 profiles from JASPAR 2022 were revised to either promote them to the CORE collection, update the associated metadata, or remove them because of validation inconsistencies or poor quality. The JASPAR database stores and focuses mostly on PFMs as the model of choice for TF-DNA interactions. More information on the methods can be found in the <a href="https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkad1059" target="_blank"> @@ -188,31 +188,31 @@ Output can be restricted to a particular region by using the -chrom, -start and -end options.</li> </ul> </p> <h4>Example: retrieve all JASPAR items in chr1:200001-200400</h4> <pre><tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/$db/jaspar/JASPAR2024.bb -chrom=chr1 -start=200000 -end=200400 stdout</tt></pre> <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="https://mencius.uio.no/JASPAR/JASPAR_genome_browser_tracks/" target="_blank">https://mencius.uio.no/JASPAR/JASPAR_genome_browser_tracks/</a>.</li> - <li>Code used to create the UCSC tracks are available at <a href="https://github.com/ievarau/JASPAR-UCSC-tracks/tree/master">https://github.com/ievarau/JASPAR-UCSC-tracks/tree/master</a>.</li> + <li>Code used to create the UCSC tracks is available at <a href="https://github.com/ievarau/JASPAR-UCSC-tracks/tree/master">https://github.com/ievarau/JASPAR-UCSC-tracks/tree/master</a>.</li> <li>The underlying JASPAR motif data is available through the JASPAR website at <a href="https://jaspar.elixir.no/" target="_blank">https://jaspar.elixir.no</a>.</li> </ul> <h2>Other Genomes</h2> <p>The JASPAR group provides TFBS predictions for many additional species and genomes. The 2026 release is available as a native track on the following genomes, and additionally on mm10 and araTha1 by connection to their <a href="../cgi-bin/hgHubConnect#publicHubs"> 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>