1e4bcfc964c6f75363370455b93822c6dd586524 gperez2 Mon Dec 18 11:46:16 2023 -0800 Updating JASPAR description page for 2024 track release, refs #31973 diff --git src/hg/makeDb/trackDb/human/jaspar.html src/hg/makeDb/trackDb/human/jaspar.html index 94fd5e8..46a5faf 100644 --- src/hg/makeDb/trackDb/human/jaspar.html +++ src/hg/makeDb/trackDb/human/jaspar.html @@ -79,33 +79,47 @@ <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> +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"> +JASPAR 2024 publication</a> or on the +<a href="https://jaspar.genereg.net/" target="_blank">JASPAR website</a>.</p> + +<p> JASPAR 2022 contains updated transcription factor binding sites -with additional transcription factor profiles. More information on -the methods can be found in their upcoming publication or on the +with additional transcription factor profiles. More information on the methods can be found in the +<a href="https://www.ncbi.nlm.nih.gov/pubmed/34850907" target="_blank"> +JASPAR 2022 publication</a> +JASPAR 2022 publication or on the <a href="https://jaspar.genereg.net/" target="_blank">JASPAR website</a>.</p> <p> JASPAR 2020 scanned DNA sequences with JASPAR CORE TF-binding profiles 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 coloring of the genome tracks and to allow for comparison of prediction confidence between different profiles.</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 <em>et al.</em> 2009). For scanning genomes with the BioPerl TFBS module, profiles were converted to PWMs and matches were kept with a @@ -143,31 +157,31 @@ target=_blank>here</a>. Run a utility with no arguments to see a brief description of the utility and its options. <ul> <li><b>bigBedInfo</b> provides summary statistics about a bigBed file including the number of items in the file. With the <b>-as</b> option, the output includes an autoSql definition of data columns, useful for interpreting the column values.</li> <li><b>bigBedToBed</b> converts the binary bigBed data to tab-separated text. 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/$db/jaspar/JASPAR2022.bb -chrom=chr1 -start=200000 -end=200400 stdout</tt></pre> +<pre><tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/$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="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" target="_blank"> https://github.com/wassermanlab/JASPAR-UCSC-tracks</a>.</li> <li>The underlying JASPAR motif data is available through the JASPAR website at <a href="https://jaspar.genereg.net/" target="_blank">https://jaspar.genereg.net/</a>.</li> </ul> @@ -274,15 +288,25 @@ target="_blank">PMC7145627</a> </p> <p> Khan A, Fornes O, Stigliani A, Gheorghe M, Castro-Mondragon JA, van der Lee R, 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> + +<p> +Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, Castro-Mondragon JA, Ferenc K, Kumar V, Lemma +RB, Lucas J, Chèneby J, Baranasic D <em>et al</em>. +<a href="https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkad1059" target="_blank"> +JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding +profiles</a>. +<em>Nucleic Acids Res</em>. 2023 Nov 14;. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/37962376" target="_blank">37962376</a> +</p>