Kun:LabNotes/CpgSeq/2011-9-27

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Analysis of the BSPP data from UCLA RO 96 blood samples

Mid-parent offspring (MPO) analysis

  • The purpose of this analysis is to quickly identify the CpG sites that exhibit heritable patterns on DNA methylation.
  • I first combined all the BED files Noi generated with allBED2Matrix.pl. I filtered out sites that has less than 40 valid methylation values or STD<0.1.
  • I then wrote a script for MPO analysis: mpo.pl, which yielded 7185 sites that could potentially be heritable. Note that the criteria are relatively loose. I only require r>=0.2 and chi-square >1.
  • Then I wrote a second script to extract the methylation values for individual CpG sites, so that I can carefully examine how well does MPO work.extract_trios_methyl_values.pl.
  • I picked a few sites that have the highest r values, and drew the scatter plots with MS-Excel. It seems to me that the correlation is modest at best even with these sites. Also when I looked up these sites on UCSC genome browser, I found that these sites are all CpG-SNPs. This sort of validated the MPO analysis. However, to identify heritable CpG sites that are not on SNPs, we will have to filter out the SNP sites prior to MPO analysis.
  • After filtering out CpG-SNPs based on snp130, the list was reduced to 4519. One example is shown below.
  File:Chr17 4559596 MPO.png