Density of ZFBS-Morph overlaps in the build canFam2 of the dog genome

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By Minou Bina1, Phillip Wyss1, Xiaohui Song2

1. Purdue University, Department of Chemistry 2. Information Technology at Purdue University

This publication provides a file (in wig.gz format) for examining the density of ZFBS-Morph overlaps at the UCSC genome browser.

Version 1.0 - published on 16 Jun 2020 doi:10.4231/P6C1-5419 - cite this Content may change until committed to the archive on 16 Jul 2020

Licensed under CC0 1.0 Universal

Description

In mammals, genomic imprinting results in the expression of a subset of genes in a parent-of-origin-specific manner.  However, despite many efforts not much is known about the number of imprinted genes in dogs and how they are controlled.  Thus, critical to understanding canine genetics is to be able to discover the positions of imprinted genes and the imprinting control regions (ICRs) in dogs.  Studies of the mouse and human genomes have revealed that 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 canFam2 of the dog 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 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 and
      • BINA_Dens_ZFBS-Morph_overlaps_dog_canFam2.wig.gz
  • To view the plots at the UCSC genome browser, go to https://genome.ucsc.edu/
  • Select the build canFam2 of the dog 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_dog_canFam2.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 of the dog genome, we found that reliable peaks encompassed 3 or more ZFBS-Morph overlaps.  Peaks encompassing 2 overlaps could be true or false positives.

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

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