Ns126:Calendar/NOTES/2015-6-26
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
- Density.CorrelationDifferenceBetweenCancerNormal.jpg
Figure 1. Density plot for the correlation of high density CpG regions in 450K array between cancer and normals
- CorrelationDifferenceBetweenCancerNormal.jpg
Figure 1. Comparison of the correlation for the high density CpG regions in 450K array between cancer and normals
- 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