Ns126:Calendar/NOTES/2015-6-26: Difference between revisions

From ZhangLabWiki
Jump to navigation Jump to search
>Shicheng
>Shicheng
Line 9: Line 9:
==Result==
==Result==


=== high density CpG regions in 450K array===
=== High density CpG regions in 450K array===




=== correlation of high density CpG regions in 450K array===
=== Correlation of high density CpG regions in 450K array===
<gallery widths=400px heights=400px>
<gallery widths=400px heights=400px>
File:Density.CorrelationDifferenceBetweenCancerNormal.jpg|Figure 1. Density plot for the correlation of high density CpG regions in 450K array between cancer and normals
File:Density.CorrelationDifferenceBetweenCancerNormal.jpg|Figure 1. Density plot for the correlation of high density CpG regions in 450K array between cancer and normals

Revision as of 22:36, 26 June 2015

Methylation Block in HM450 microarray

Motivation

Dr.Zhang tried defined methylation haplotype and methylation blocks with GWBS data. and we are sure that these regions must have special biological, genomic or evolution functions. Therefore, I want to do the similar analysis in HM450K array. I will compare the regions identified in HM450 with the regions disovered by Dr. Zhang. In our hypothesis, the regions in my analysis would be a sutset of Dr. Zhang's regions.

Method

I collected pair-wised samples of 11 cancers from TCGA project.

Result

High density CpG regions in 450K array

Correlation of high density CpG regions in 450K array

  • high correction region based on methylation 450K dataset
  • GSE53045 ( 50 smokers and 61 non-smokers, PBMC)
  • GSE32148 ()
  • GSE35069 Differential DNA Methylation in Purified Human Blood Cells
  • GSE36054 Methylation Profiling of Blood DNA from Healthy Children
  • GSE36064 Methylation Profiling of Blood DNA from Healthy Children (Harvard Age Study)
  • GSE41169 Blood DNA methylation profiles in a Dutch population
  • GSE44132 Antenatal Blood DNA Methylation Profiles
  • GSE42861


It is very interesting result: 1) cancer have two peak 2) cancer have more higher correction regions