Density of ZFBS-Morph overlaps in the build hg19 of the human genome

<p>Genomic imprinting results in the expression of a subset of genes from either the maternal or paternal allele.  This process is regulated by Imprinting Control Regions (ICRs), dispersed along the mammalian autosomal chromosomes.  The ICRs often encompass a set of composite DNA elements consisting of the ZFP57 binding site (ZFBS) overlapping a subset of the MLL1 morphemes.  These elements (ZFBS-Morph overlaps) usually occur as clusters of 2 or more in ICRs and germline Differentially Methylated Regions (gDMRs).  To enhance detection of such clusters, we created plots for displaying the density of ZFBS-Morph overlaps along the build hg19 of the human genome.</p>

<p>This publication provides a file (in wig.gz format) for examining the density of ZFBS-Morph overlaps at the UCSC genome browser.  Follow the steps listed below to obtain a copy of the file for creating a custom track at the browser.</p>

<ul>
<li>At the top right corner of this page, click on download bundle. The file is compressed.</li>
<li>After download, decompress the file.
<ul>
<li>You will find two files named:
<ul>
<li>Readme.txt</li>
<li>BINA_Dens_ZFBS-Morph_overlaps_hg19.wig.gz</li>
</ul>
</li>
</ul>
</li>
</ul>

<ul>
<li>To view the plots at the UCSC genome browser, go to <a href="https://genome.ucsc.edu/">https://genome.ucsc.edu/</a></li>
</ul>

<ul>
<li>Select the build hg19 of the human genome. 
<ul>
<li>You will find a map displaying the default tracks.</li>
</ul>
</li>
</ul>

<ul>
<li>Under the map, click on "manage custom tracks”
<ul>
<li>Afterward, click on "add custom track"</li>
<li>Then click on choose file. </li>
</ul>
</li>
</ul>

<p>*On your computer, select the file named BINA_Dens_ZFBS-Morph_overlaps_hg19.wig.gz </p>

<ul>
<li>Subsequently, click on submit.</li>
</ul>

<p>At the browser, the plot will display the density-peaks as brown vertical bars.</p>

<ul>
<li>NOTE: the track will indicate “no data” in regions that do not include any density-peak.
<p>In evaluations, we found that reliable peaks encompassed 3 or more ZFBS-Morph overlaps.  Peaks encompassing 2 overlaps could be true or false positive.</p>

<p> </p>
</li>
</ul>

<p>If you observe anomalies on this page, please contact bina@ purdue.edu</p>