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

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By Minou Bina1, Phillip J. Wyss1, Xiaohui Carol Song1

Purdue University

Supplementary material for the publication entitled “Discovering candidate imprinted genes and Imprinting Control Regions in the human genome” Bina M. bioRxiv (2019), doi: 10.1101/678151.

Version 1.0 - published on 30 May 2019 doi:10.4231/PR3C-J556 - cite this Archived on 30 Jun 2019

Licensed under CC0 1.0 Universal

Description

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.

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.

  • At the top right corner of this page, click on download bundle. The file is compressed.
  • After download, decompress the file.
    • You will find two files named:
      • Readme.txt
      • BINA_Dens_ZFBS-Morph_overlaps_hg19.wig.gz
  • Select the build hg19 of the human genome. 
    • You will find a map displaying the default tracks.
  • Under the map, click on "manage custom tracks”
    • Afterward, click on "add custom track"
    • Then click on choose file. 

*On your computer, select the file named BINA_Dens_ZFBS-Morph_overlaps_hg19.wig.gz 

  • Subsequently, click on submit.

At the browser, the plot will display the density-peaks as brown vertical bars.

  • NOTE: the track will indicate “no data” in regions that do not include any density-peak.

    In evaluations, we found that reliable peaks encompassed 3 or more ZFBS-Morph overlaps.  Peaks encompassing 2 overlaps could be true or false positive.

     

If you observe anomalies on this page, please contact bina@ purdue.edu

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