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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
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<title>RnBeads</title>
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<li><a href="methylomes.html">Methylome Resource</a></li>
<li class="active"><a href="regions.html">Region Sets</a></li>
<li><a href="ageprediction.html">Age Prediction</a></li>
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<h1 class="mt-4 mb-3">Region Set Resource</h1>
<div class="row">
<div class="col-md-12">
<p>This reference stores a number of useful region set annotations to be used in <a href="index.html">RnBeads</a> analyses. You can find a list of available region sets along with their descriptions below. Here is an example showing how you can employ them in your analyses:</p>
<pre class="pre-scrollable">
REGION_SET <- "tiling1kb"
ASSEMBLY <- "hg19"
rnb.load.annotation.from.db(REGION_SET, assembly=ASSEMBLY)
rnb.options(region.types=union(rnb.getOption("region.types"), REGION_SET))
</pre>
</div>
</div>
<div class="row">
<div class="col-md-12">
<table class="table table-hover">
<thead>
<tr>
<th>Region Set</th>
<th>Assembly</th>
<th>File</th>
<th>N</th>
<th>Description</th>
</tr>
</thead>
<tbody>
<tr>
<td>tiling</td>
<td>hg19</td>
<td>[native]</td>
<td>619146</td>
<td>Genome tiling regions of length 5000</td>
</tr>
<tr>
<td>genes</td>
<td>hg19</td>
<td>[native]</td>
<td>57736</td>
<td>Ensembl genes, version Ensembl Genes 75</td>
</tr>
<tr>
<td>promoters</td>
<td>hg19</td>
<td>[native]</td>
<td>57736</td>
<td>Promoter regions of Ensembl genes, version Ensembl Genes 75</td>
</tr>
<tr>
<td>cpgislands</td>
<td>hg19</td>
<td>[native]</td>
<td>27718</td>
<td>CpG island track of the UCSC Genome browser</td>
</tr>
<tr>
<td>tiling200bp</td>
<td>hg19</td>
<td><a href="./materials//data/regiondb/annotation_hg19_tiling200bp.RData">download</a></td>
<td>15478399</td>
<td>Genome tiling regions using a window size of 200bp</td>
</tr>
<tr>
<td>tiling500bp</td>
<td>hg19</td>
<td><a href="./materials//data/regiondb/annotation_hg19_tiling500bp.RData">download</a></td>
<td>6191368</td>
<td>Genome tiling regions using a window size of 500bp</td>
</tr>
<tr>
<td>tiling1kb</td>
<td>hg19</td>
<td><a href="./materials//data/regiondb/annotation_hg19_tiling1kb.RData">download</a></td>
<td>3095689</td>
<td>Genome tiling regions using a window size of 1kb</td>
</tr>
<tr>
<td>tiling10kb</td>
<td>hg19</td>
<td><a href="./materials//data/regiondb/annotation_hg19_tiling10kb.RData">download</a></td>
<td>309579</td>
<td>Genome tiling regions using a window size of 10kb</td>
</tr>
<tr>
<td>ensembleRegBuildBPall</td>
<td>hg19</td>
<td><a href="./materials//data/regiondb/annotation_hg19_ensembleRegBuildBPall.RData">download</a></td>
<td>613343</td>
<td>Ensembl Regulatory build from BLUEPRINT data release 20150128 -- all</td>
</tr>
<tr>
<td>ensembleRegBuildBPctcf</td>
<td>hg19</td>
<td><a href="./materials//data/regiondb/annotation_hg19_ensembleRegBuildBPctcf.RData">download</a></td>
<td>78648</td>
<td>Ensembl Regulatory build from BLUEPRINT data release 20150128 -- ctcf</td>
</tr>
<tr>
<td>ensembleRegBuildBPdistal</td>
<td>hg19</td>
<td><a href="./materials//data/regiondb/annotation_hg19_ensembleRegBuildBPdistal.RData">download</a></td>
<td>169651</td>
<td>Ensembl Regulatory build from BLUEPRINT data release 20150128 -- distal</td>
</tr>
<tr>
<td>ensembleRegBuildBPdnase</td>
<td>hg19</td>
<td><a href="./materials//data/regiondb/annotation_hg19_ensembleRegBuildBPdnase.RData">download</a></td>
<td>51267</td>
<td>Ensembl Regulatory build from BLUEPRINT data release 20150128 -- dnase</td>
</tr>
<tr>
<td>ensembleRegBuildBPproximal</td>
<td>hg19</td>
<td><a href="./materials//data/regiondb/annotation_hg19_ensembleRegBuildBPproximal.RData">download</a></td>
<td>146789</td>
<td>Ensembl Regulatory build from BLUEPRINT data release 20150128 -- proximal</td>
</tr>
<tr>
<td>ensembleRegBuildBPtfbs</td>
<td>hg19</td>
<td><a href="./materials//data/regiondb/annotation_hg19_ensembleRegBuildBPtfbs.RData">download</a></td>
<td>141385</td>
<td>Ensembl Regulatory build from BLUEPRINT data release 20150128 -- tfbs</td>
</tr>
<tr>
<td>ensembleRegBuildBPtss</td>
<td>hg19</td>
<td><a href="./materials//data/regiondb/annotation_hg19_ensembleRegBuildBPtss.RData">download</a></td>
<td>25603</td>
<td>Ensembl Regulatory build from BLUEPRINT data release 20150128 -- tss</td>
</tr>
<tr>
<td>deepGC19promoters</td>
<td>hg19</td>
<td><a href="./materials//data/regiondb/annotation_hg19_deepGC19promoters.RData">download</a></td>
<td>57783</td>
<td>DEEP reference genes derived from Gencode 19 gene annotations. Promotor annotation. Promoters are defined as 1500 bp upstream to 500 downstream of the TSS.</td>
</tr>
<tr>
<td>deepGC19genes</td>
<td>hg19</td>
<td><a href="./materials//data/regiondb/annotation_hg19_deepGC19genes.RData">download</a></td>
<td>57783</td>
<td>DEEP reference genes derived from Gencode 19 gene annotations. Gene annotation.</td>
</tr>
<tr>
<td>dynamicMethZiller2013</td>
<td>hg19</td>
<td><a href="./materials//data/regiondb/annotation_hg19_dynamicMethZiller2013.RData">download</a></td>
<td>716087</td>
<td>Dynamically methylated regions extracted from Ziller, et al. (2013). Nature, 500(7463), 477â481. http://doi.org/10.1038/nature12433. Assembly: hg19</td>
</tr>
<tr>
<td>tiling</td>
<td>hg38</td>
<td>[native]</td>
<td>617665</td>
<td>Genome tiling regions of length 5000</td>
</tr>
<tr>
<td>genes</td>
<td>hg38</td>
<td>[native]</td>
<td>60070</td>
<td>Ensembl genes, version Ensembl Genes 78</td>
</tr>
<tr>
<td>promoters</td>
<td>hg38</td>
<td>[native]</td>
<td>60070</td>
<td>Promoter regions of Ensembl genes, version Ensembl Genes 78</td>
</tr>
<tr>
<td>cpgislands</td>
<td>hg38</td>
<td>[native]</td>
<td>27949</td>
<td>CpG island track of the UCSC Genome browser</td>
</tr>
<tr>
<td>tiling200bp</td>
<td>hg38</td>
<td><a href="./materials//data/regiondb/annotation_hg38_tiling200bp.RData">download</a></td>
<td>15441361</td>
<td>Genome tiling regions using a window size of 200bp</td>
</tr>
<tr>
<td>tiling500bp</td>
<td>hg38</td>
<td><a href="./materials//data/regiondb/annotation_hg38_tiling500bp.RData">download</a></td>
<td>6176550</td>
<td>Genome tiling regions using a window size of 500bp</td>
</tr>
<tr>
<td>tiling1kb</td>
<td>hg38</td>
<td><a href="./materials//data/regiondb/annotation_hg38_tiling1kb.RData">download</a></td>
<td>3088281</td>
<td>Genome tiling regions using a window size of 1kb</td>
</tr>
<tr>
<td>tiling10kb</td>
<td>hg38</td>
<td><a href="./materials//data/regiondb/annotation_hg38_tiling10kb.RData">download</a></td>
<td>308837</td>
<td>Genome tiling regions using a window size of 10kb</td>
</tr>
<tr>
<td>ensembleRegBuildBPall</td>
<td>hg38</td>
<td><a href="./materials//data/regiondb/annotation_hg38_ensembleRegBuildBPall.RData">download</a></td>
<td>528248</td>
<td>Ensembl Regulatory build from BLUEPRINT data release 20150820 -- all</td>
</tr>
<tr>
<td>ensembleRegBuildBPctcf</td>
<td>hg38</td>
<td><a href="./materials//data/regiondb/annotation_hg38_ensembleRegBuildBPctcf.RData">download</a></td>
<td>116838</td>
<td>Ensembl Regulatory build from BLUEPRINT data release 20150820 -- ctcf</td>
</tr>
<tr>
<td>ensembleRegBuildBPdistal</td>
<td>hg38</td>
<td><a href="./materials//data/regiondb/annotation_hg38_ensembleRegBuildBPdistal.RData">download</a></td>
<td>197516</td>
<td>Ensembl Regulatory build from BLUEPRINT data release 20150820 -- distal</td>
</tr>
<tr>
<td>ensembleRegBuildBPdnase</td>
<td>hg38</td>
<td><a href="./materials//data/regiondb/annotation_hg38_ensembleRegBuildBPdnase.RData">download</a></td>
<td>54016</td>
<td>Ensembl Regulatory build from BLUEPRINT data release 20150820 -- dnase</td>
</tr>
<tr>
<td>ensembleRegBuildBPproximal</td>
<td>hg38</td>
<td><a href="./materials//data/regiondb/annotation_hg38_ensembleRegBuildBPproximal.RData">download</a></td>
<td>95397</td>
<td>Ensembl Regulatory build from BLUEPRINT data release 20150820 -- proximal</td>
</tr>
<tr>
<td>ensembleRegBuildBPtfbs</td>
<td>hg38</td>
<td><a href="./materials//data/regiondb/annotation_hg38_ensembleRegBuildBPtfbs.RData">download</a></td>
<td>40751</td>
<td>Ensembl Regulatory build from BLUEPRINT data release 20150820 -- tfbs</td>
</tr>
<tr>
<td>ensembleRegBuildBPtss</td>
<td>hg38</td>
<td><a href="./materials//data/regiondb/annotation_hg38_ensembleRegBuildBPtss.RData">download</a></td>
<td>23730</td>
<td>Ensembl Regulatory build from BLUEPRINT data release 20150820 -- tss</td>
</tr>
<tr>
<td>gencode22promoters</td>
<td>hg38</td>
<td><a href="./materials//data/regiondb/annotation_hg38_gencode22promoters.RData">download</a></td>
<td>60446</td>
<td>Reference annotation derived from Gencode 22 gene annotations. Gene annotation. Promotor annotation. Promoters are defined as 1500 bp upstream to 500 downstream of the TSS.</td>
</tr>
<tr>
<td>gencode22genes</td>
<td>hg38</td>
<td><a href="./materials//data/regiondb/annotation_hg38_gencode22genes.RData">download</a></td>
<td>60446</td>
<td>Reference annotation derived from Gencode 22 gene annotations. Gene annotation.</td>
</tr>
<tr>
<td>dynamicMethZiller2013</td>
<td>hg38</td>
<td><a href="./materials//data/regiondb/annotation_hg38_dynamicMethZiller2013.RData">download</a></td>
<td>716087</td>
<td>Dynamically methylated regions extracted from Ziller, et al. (2013). Nature, 500(7463), 477â481. http://doi.org/10.1038/nature12433. Assembly: hg38. liftOver from hg19.</td>
</tr>
<tr>
<td>tiling</td>
<td>mm9</td>
<td>[native]</td>
<td>530988</td>
<td>Genome tiling regions of length 5000</td>
</tr>
<tr>
<td>genes</td>
<td>mm9</td>
<td>[native]</td>
<td>37583</td>
<td>Ensembl genes, version Ensembl Genes 67</td>
</tr>
<tr>
<td>promoters</td>
<td>mm9</td>
<td>[native]</td>
<td>37583</td>
<td>Promoter regions of Ensembl genes, version Ensembl Genes 67</td>
</tr>
<tr>
<td>cpgislands</td>
<td>mm9</td>
<td>[native]</td>
<td>15991</td>
<td>CpG island track of the UCSC Genome browser</td>
</tr>
<tr>
<td>tiling200bp</td>
<td>mm9</td>
<td><a href="./materials//data/regiondb/annotation_mm9_tiling200bp.RData">download</a></td>
<td>13274487</td>
<td>Genome tiling regions using a window size of 200bp</td>
</tr>
<tr>
<td>tiling500bp</td>
<td>mm9</td>
<td><a href="./materials//data/regiondb/annotation_mm9_tiling500bp.RData">download</a></td>
<td>5309802</td>
<td>Genome tiling regions using a window size of 500bp</td>
</tr>
<tr>
<td>tiling1kb</td>
<td>mm9</td>
<td><a href="./materials//data/regiondb/annotation_mm9_tiling1kb.RData">download</a></td>
<td>2654907</td>
<td>Genome tiling regions using a window size of 1kb</td>
</tr>
<tr>
<td>tiling10kb</td>
<td>mm9</td>
<td><a href="./materials//data/regiondb/annotation_mm9_tiling10kb.RData">download</a></td>
<td>265500</td>
<td>Genome tiling regions using a window size of 10kb</td>
</tr>
<tr>
<td>tiling</td>
<td>mm10</td>
<td>[native]</td>
<td>545114</td>
<td>Genome tiling regions of length 5000</td>
</tr>
<tr>
<td>genes</td>
<td>mm10</td>
<td>[native]</td>
<td>43309</td>
<td>Ensembl genes, version ENSEMBL GENES 79 (SANGER UK)</td>
</tr>
<tr>
<td>promoters</td>
<td>mm10</td>
<td>[native]</td>
<td>43309</td>
<td>Promoter regions of Ensembl genes, version ENSEMBL GENES 79 (SANGER UK)</td>
</tr>
<tr>
<td>cpgislands</td>
<td>mm10</td>
<td>[native]</td>
<td>16009</td>
<td>CpG island track of the UCSC Genome browser</td>
</tr>
<tr>
<td>tiling200bp</td>
<td>mm10</td>
<td><a href="./materials//data/regiondb/annotation_mm10_tiling200bp.RData">download</a></td>
<td>13627618</td>
<td>Genome tiling regions using a window size of 200bp</td>
</tr>
<tr>
<td>tiling500bp</td>
<td>mm10</td>
<td><a href="./materials//data/regiondb/annotation_mm10_tiling500bp.RData">download</a></td>
<td>5451055</td>
<td>Genome tiling regions using a window size of 500bp</td>
</tr>
<tr>
<td>tiling1kb</td>
<td>mm10</td>
<td><a href="./materials//data/regiondb/annotation_mm10_tiling1kb.RData">download</a></td>
<td>2725532</td>
<td>Genome tiling regions using a window size of 1kb</td>
</tr>
<tr>
<td>tiling10kb</td>
<td>mm10</td>
<td><a href="./materials//data/regiondb/annotation_mm10_tiling10kb.RData">download</a></td>
<td>272564</td>
<td>Genome tiling regions using a window size of 10kb</td>
</tr>
</tbody>
</table>
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