Ns126:Calendar/NOTES/2015-7-12

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Revision as of 07:41, 21 July 2015 by >Shicheng (→‎Relationship between MHL and Methylation entropy)
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Materials and Method[edit]

Dr. Zhang update the MONOD methylation haplotype result and therefore I can check the latest result in the relationship between samples and check the distinguish ability of cancer and normals based on methylation haplotype load.

About the data processing, check: http://genome-tech.ucsd.edu/LabNotes/index.php/Kun:LabNotes/MONOD/2015-7-6

Result[edit]

MHL Distrbution in 3 dataaset[edit]


Relationship between samples in the propestive of hierarchical clustering based on MHL[edit]

N37<-c("Colon","Frontal lobe","Heart","Small intestine","Liver","Lung","Skeletal muscle","Pancrease","Stomach")
N37<-c("LymphNodes","Blood","Colon","BrainCRBM","Heart","Liver","Lung","Muscle","Pancreas","Stomach") # modified


  • consider: batch differences in read depth, read length or other artifacts.

Relationship between samples in the propestive of PCA analysis based on MHL[edit]

File:WGBS.MONOD.PCA.2.jpeg

Functional enrichment of the loci that have the highest loading to PC1 and PC2[edit]

Methylation 450K sample with CD, ESC and Cancer sample in the sapce of PC1 and PC2[edit]

Relationship between MHL and Methylation entropy[edit]

Definition[edit]

File:Methylation.Entropy.jpg