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)
</gallery>
 
 
<gallery widths=400px heights=400px>
File:RRBS.Boxplot.pahse2.jpeg|Figure 1C. Boxplot for the distribution of MHL in RRBS dataset
File:SeqCap.phase2.boxplot.jpeg|Figure 1D. Boxplot for the distribution of MHL in SeqCap dataset
</gallery>
</gallery>


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===Relationship between MHL and Methylation entropy===
===Relationship between MHL and Methylation entropy===
====Definition====
[[File:Methylation.Entropy.jpg]]

Latest revision as of 07:41, 21 July 2015

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