Ns126:Calendar/NOTES/2015-7-12: Difference between revisions

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<gallery widths=800px heights=400px>
<gallery widths=800px heights=400px>
File:WGBS.Boxplot.phase2.withcancer.jpeg|Figure 1A-2. Boxplot for the distribution of MHL in WGBS dataset(total)
File:WGBS.Boxplot.phase2.withcancer.jpeg|Figure 1A-1. Boxplot for the distribution of MHL in WGBS dataset(total)
File:WGBS.Boxplot.phase2.jpg.jpeg|Figure 1A-1. Boxplot for the distribution of MHL in WGBS dataset(part)
File:WGBS.Boxplot.phase2.jpg.jpeg|Figure 1A-2. Boxplot for the distribution of MHL in WGBS dataset(part)
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</gallery>



Revision as of 06:58, 21 July 2015

Materials and Method

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

MHL Distrbution in 3 dataaset

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

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

File:WGBS.MONOD.PCA.2.jpeg

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

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

Relationship between MHL and Methylation entropy