HepG2 and K562 cCRE syntenic ages

<p>### DESCRIPTION ###</p> <p>HepG2 and K562 ENCODE 3 cCRE pELS, dELS,&nbsp;pELS + CTCF, dELS +CTCF.</p> <p>### METHOD ###</p> <p>To assign sequence ages enhancer cCRE&nbsp;.bed coordinates were intersected with hg38 100-way multiZ alignment&nbsp;syntenic blocks from UCSC genome browser.</p> <p>&nbsp;</p> <p>### Column names ###</p> <p>[#chr&nbsp;&nbsp; &nbsp;start_syn&nbsp;&nbsp; &nbsp;end_syn&nbsp;&nbsp; &nbsp;enh_id&nbsp;&nbsp; &nbsp;#chr_enh&nbsp;&nbsp; &nbsp;start_enh&nbsp;&nbsp; &nbsp;end_enh&nbsp;&nbsp; &nbsp;segment_number&nbsp;&nbsp; &nbsp;simple_0_complex_1&nbsp;&nbsp; &nbsp;core_0_derived_1&nbsp;&nbsp; &nbsp;mrca_age]</p> <p>### explanation of column names ###</p> <p>[#chr&nbsp;&nbsp; &nbsp;start_syn&nbsp;&nbsp; &nbsp;end_syn]: syntenic block .bed coordinates in hg38</p> <p>[&nbsp;enh_id&nbsp;&nbsp; &nbsp;#chr_enh&nbsp;&nbsp; &nbsp;start_enh&nbsp;&nbsp; &nbsp;end_enh]: cCRE .bed coordinates in hg38</p> <p>[segment_number]:&nbsp;We count the number of syntenic block segments&nbsp;overlapping a single enhancer.&nbsp;</p> <p>[simple_0_complex_1]:&nbsp;Some syntenic blocks overlap multiple syntenic blocks, which we term &quot;complex&quot;. Others overlap a single syntenic block, which we term &quot;simple&quot;. Complex elements are annotated with 1 and simple elements are annotated with 0.&nbsp;</p> <p>[core_0_derived_1]:&nbsp;In complex enhancer sequences (i.e. enhancer sequences with multiple sequence ages).&nbsp;We refer to the&nbsp;oldest sequence in an enhancer is the &quot;core&quot; (annotated as 1) and the&nbsp;younger sequence age(s) as &quot;derived&quot; (annotated as 0).&nbsp;</p> <p>[mrca_age]:&nbsp;For each syntenic segment, we annotate the most recent common ancestor (MRCA) age. This corresponds to the estimated branch length between humans and the related MRCA.&nbsp;</p> <p>Taxon and summarized taxon (&quot;Taxon2&quot;)&nbsp;for each MRCA age is annotated in the&nbsp;hg38_syn_taxon.bed file.&nbsp;</p>