c27d515b7e62073ec2834f789f423d757e91b75d gperez2 Mon Mar 30 17:16:33 2026 -0700 Made some updates to the mm10 ENCODE4 cCREs track description page, refs #37131 diff --git src/hg/makeDb/trackDb/mouse/mm10/cCREregistry.html src/hg/makeDb/trackDb/mouse/mm10/cCREregistry.html index 3a7d359f233..22a47c8fbbd 100644 --- src/hg/makeDb/trackDb/mouse/mm10/cCREregistry.html +++ src/hg/makeDb/trackDb/mouse/mm10/cCREregistry.html @@ -6,77 +6,77 @@ DNase hypersensitive sites further annotated with histone modifications (H3K4me3 and H3K27ac) or CTCF binding measured by ChIP-seq experiments. In this latest version of the Registry (V4), the representative DNase hypersensitive sites (rDHSs) were supplemented with 7,658 representative transcription factor ChIP-seq peaks (TF rPeaks)—peaks that represent binding sites for at least five TFs. The Registry of cCREs is one of the core components of the integrative level of the ENCODE Encyclopedia of DNA Elements.</p> <p>Additional exploration of the cCREs and underlying raw ENCODE signal data can be done with the <b>Core Collection</b> track. The data is also available on the <a target="_blank" href="https://screen.wenglab.org/">SCREEN</a> (Search Candidate cis-Regulatory Elements) web tool, designed specifically for the Registry, accessible by item mouseovers and linkouts from the track details page.</p> <h2>Display Conventions and Configurations</h2> <p> -Each cCRE is displayed as a colored box by type, which reflects its putative functional assignment -based on biochemical signatures and genomic context:</p> -<p> -<img src="../images/encode4cCREs.png" alt="Graphic of cCRE classifications" width="40%"></p> -<p> -Mousing over the data will display the accession ID, the assigned cCRE class type, and the Max-Z scores -for the various underlying biosignals (DNase, H3K4me3, H3K27ac, CTCF). A track filter is also available -to selectively show items based on their cCRE class type.</p> - -<h2>Methods</h2> -<p> -Candidate cis-regulatory elements (cCREs) were first anchored on nucleosome-sized DNase -hypersensitive sites (rDHSs) identified from DNase-seq data. These rDHSs were then annotated -using ChIP-seq data for histone modifications—H3K4me3 and H3K27ac, marking promoters and -enhancers, respectively—and CTCF, marking insulators. To supplement rDHS-anchored cCRE -definitions, transcription factor ChIP-seq peaks were incorporated, enabling identification -of cCREs even in regions of low chromatin accessibility. Although not used for anchoring, -ATAC-seq data were used to assess chromatin accessibility in biosamples lacking DNase-seq.</p> - -<p> -Classification of cCREs was performed based on the following criteria:</p> +Each cCRE is color-coded by its classification type, which reflects its putative functional +assignment based on biochemical signatures and genomic context:</p> <ol> <li><strong><span style="color: #ff0000;">Promoter-like signatures (promoter)</span></strong> must fall within 200 bp of a TSS and have high chromatin accessibility and H3K4me3 signals.</li> <li><strong><span style="color: #ffa700;">TSS-proximal enhancer-like signatures (proximal enhancer)</span></strong> have high chromatin accessibility and H3K27ac signals and are within 2 kb of an annotated TSS. If they are within 200 bp of a TSS, they must also have low H3K4me3 signal.</li> <li><strong><span style="color: #ffcd00;">TSS-distal enhancer-like signatures (distal enhancer)</span></strong> have high chromatin accessibility and H3K27ac signals and are farther than 2 kb from an annotated TSS.</li> <li><span style="color: #ffaaaa;"><strong>Chromatin accessibility + H3K4me3 (CA-H3K4me3)</strong></span> have high chromatin accessibility and H3K4me3 signals but low H3K27ac signals and do not fall within 200 bp of a TSS.</li> <li><span style="color: #00b0f0;"><strong>Chromatin accessibility + CTCF (CA-CTCF)</strong></span> have high chromatin accessibility and CTCF signals but low H3K4me3 and H3K27ac signals.</li> <li><span style="color: #be28e5;"><strong>Chromatin accessibility + transcription factor (CA-TF)</strong></span> have high chromatin accessibility, low H3K4me3, H3K27ac, and CTCF signals, and are bound by a transcription factor.</li> <li><span style="color: #06da93;"><strong>Chromatin accessibility (CA)</strong></span> have high chromatin accessibility and low H3K4me3, H3K27ac, and CTCF signals.</li> <li><span style="color: #d876ec;"><strong>Transcription factor (TF)</strong></span> have low chromatin accessibility, low H3K4me3, H3K27ac, and CTCF signals and are bound by a transcription factor.</li> </ol> +<p> +Mousing over the data will display the accession ID, the assigned cCRE class type, and the Max-Z scores +for the various underlying biosignals (DNase, H3K4me3, H3K27ac, CTCF). A track filter is also available +to selectively show items based on their cCRE class type.</p> + +<h2>Methods</h2> +<p> +Candidate cis-regulatory elements (cCREs) were first anchored on nucleosome-sized DNase +hypersensitive sites (rDHSs) identified from DNase-seq data. These rDHSs were then annotated +using ChIP-seq data for histone modifications—H3K4me3 and H3K27ac, marking promoters and +enhancers, respectively—and CTCF, marking insulators. To supplement rDHS-anchored cCRE +definitions, transcription factor ChIP-seq peaks were incorporated, enabling identification +of cCREs even in regions of low chromatin accessibility. Although not used for anchoring, +ATAC-seq data were used to assess chromatin accessibility in biosamples lacking DNase-seq.</p> + +<p> +The following diagram illustrates the biochemical signal patterns used to classify each cCRE type:</p> +<p> +<img src="../images/encode4cCREs.png" alt="Graphic of cCRE classifications" width="40%"></p> <h2>Data Access</h2> <p> The ENCODE accession numbers of the constituent datasets at the <a target="_blank" href="https://encodeproject.org/">ENCODE Portal</a> are available from the cCRE details page.</p> <p> The data in this track can be interactively explored with the <a target="_blank" href="/cgi-bin/hgTables">Table Browser</a> or the <a target="_blank" href="/cgi-bin/hgIntegrator">Data Integrator</a>. The data can be accessed from scripts through our <a target="_blank" href="https://api.genome.ucsc.edu/">API</a>, the track name is "cCREregistry".</p> <p> For automated download and analysis, this annotation is stored in a bigBed file that can be downloaded from <a target="_blank" href="http://hgdownload.soe.ucsc.edu/gbdb/mm10/encode4/ccre/">our download server</a>.