2c78d69bf51c0282d97dd262b8f9005f1c5d3192 kate Tue May 12 16:32:36 2020 -0700 Polish track config and draft track description. refs #24668 diff --git src/hg/makeDb/trackDb/encodeCcreCombined.html src/hg/makeDb/trackDb/encodeCcreCombined.html new file mode 100644 index 0000000..813681f --- /dev/null +++ src/hg/makeDb/trackDb/encodeCcreCombined.html @@ -0,0 +1,151 @@ +<h2>Description</h2> +<p> +This track displays the <em>ENCODE Registry of candidate cis-Regulatory Elements</em> (cCREs) in +the human genome, a total of 926,535 elements identified and classified by the +ENCODE Data Analysis Center according to regulatory effect. +cCREs are the subset of DNase hypersensitivity sites clustered across all ENCODE samples +that are supported by either histone modifications (H3K4me3 and H3K27ac) or CTCF-binding data. +The cCRE dataset is the core of the integrative level of epigenomic and transcriptomic +annotations produced by ENCODE. +</p> +Additional exploration of the cCRE's and underlying raw ENCODE data is provided by 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 linkouts from the track details page. + +<!-- +<p> +The related cCREs by Biosample composite track presents ccREs +and associated epigenetic signal in all individual biosamples in a large matrix. +Additional views of the data are provided by the <a>ENCODE Integrative Megahub</a>. +</p> +--> + +<h2>Display Conventions and Configuration</h2> +<p> +CCREs are colored according to classification by regulatory signature: +<p> +<table cellpadding='2'> + + <tr> + <th style="border-bottom: 2px solid;">Color</th> + <th style="border-bottom: 2px solid;"></th> + <th style="border-bottom: 2px solid;">Group</th> + <th style="border-bottom: 2px solid;"></th> + </tr> + </thead> + +<tr><td style='background-color: red;'></td><td>red</td> + <td>promoter-like</td> + <td>PLS</td></tr> +<tr><td style='background-color: orange;'></td><td>orange</td> + <td>proximal enhancer-like</td> + <td>pELS</td></tr> +<tr><td style='background-color: yellow;'></td><td>yellow</td> + <td>distal enhancer-like</td> + <td>dELS</td></tr> +<tr><td style='background-color: blue;'</td><td>blue</td> + <td>CTCF-only</td> + <td>CTCF-only</td></tr> +<tr><td style='background-color: #ffa0a0;'></td><td>pink</td> + <td>DNase-H3K4me3</td> + <td>DNase-H3K4me3</td></tr> +</table> +</p> + +<h2>Methods</h2> +<p> +All individual DNase hypsersensitivity sites (DHSs) identified from 706 DNAse-seq experiments +in human (a total of 93 million) were iteratively clustered and filtered +for highest signal across all experiments, producing 2.2 million representative DHSs (rDHSs). +The highest signal elements from this set that were also supported by high H3K4me3, H3K27ac +and/or CTCF ChIP-seq signals were designated cCRE's (a total of 926,535 in human). +</p> +<p> +Classification of cCRE's was performed based on the following criteria: +<p> +<p> +1. cCREs with promoter-like signatures (cCRE-PLS) fall within 200 bp of +an annotated GENCODE TSS and have high DNase and H3K4me3 signals. +</p> +<p> +2. cCREs with enhancer-like signatures (cCRE-ELS) have high DNase and H3K27ac +with low H3K4me3 max-Z score if they are within 200 bp of an annotated TSS. +The subset of cCREs-ELS within 2 kb of a TSS is denoted proximal (cCRE-pELS), +while the remaining subset is denoted distal (cCRE-dELS). +</p> + +<p> +3. DNase-H3K4me3 cCREs have high H3K4me3 max-Z scores but low H3K27ac max-Z scores +and do not fall within 200 bp of a TSS. +</p> + +<p> +4. CTCF-only cCREs have high DNase and CTCF and low H3K4me3 and H3K27ac. +</p> + +<img style='margin-left: 40px;' height=229 width=371 src="../images/cCREgroups.png"> + +<p> +For further detail about the identification and classification of ENCODE cCREs see +the <i>About</i> page of the +<a target="_blank" href="https://screen.encodeproject.org">SCREEN</a> web tool. +</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 href="../cgi-bin/hgTables">Table Browser</a> or the +<a href="../cgi-bin/hgIntegrator">Data Integrator</a>. +The data can be accessed from scripts through our +<a href="https://api.genome.ucsc.edu">API</a>, the track name is "encodeCcreCombined". + +<p> +For automated download and analysis, this annotation is stored in a bigBed file that +can be downloaded from +<a href="http://hgdownload.soe.ucsc.edu/gbdb/$db/bbi/" target="_blank">our download server</a>. +The file for this track is called <tt>encodeCcreCombined.bb</tt>. +Individual regions or the whole genome annotation can be obtained using our tool +<tt>bigBedToBed</tt> which can be compiled from the source code or downloaded as a precompiled +binary for your system. +Instructions for downloading source code and binaries can be found +<a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">here</a>. +The tool can also be used to obtain only features within a given range, e.g. +<tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/bbi/encodeCcreCombined.bb -chrom=chr21 -start=0 -end=100000000 stdout</tt></p> +</p> + +<h2>Credits</h2> +<p> +This dataset was produced by the ENCODE Data Analysis Center ( +<a target="_blank" href="https://www.umassmed.edu/zlab/">Zlab</a> + at UMass Medical Center). +Thanks to Henry Pratt, Jill Moore, Michael Purcaro, and Zhiping Weng, PI for providing +this data. +Thanks also to the ENCODE Consortium, the ENCODE production laboratories, +and the ENCODE Data Coordination Center for generating and processing the datasets used here. +</p> + +<h2>References</h2> +<p> +ENCODE Project Consortium.. +<a href="https://doi.org/10.1038/nature11247" target="_blank"> +An integrated encyclopedia of DNA elements in the human genome</a>. +<em>Nature</em>. 2012 Sep 6;489(7414):57-74. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/22955616" target="_blank">22955616</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439153/" target="_blank">PMC3439153</a> +</p> + +ENCODE Project Consortium.. +<a href="http://dx.plos.org/10.1371/journal.pbio.1001046" target="_blank"> +A user's guide to the encyclopedia of DNA elements (ENCODE)</a>. +<em>PLoS Biol</em>. 2011 Apr;9(4):e1001046. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/21526222" target="_blank">21526222</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3079585/" target="_blank">PMC3079585</a> +</p> +