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

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>Shicheng
>Shicheng
 
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==Materials and Method==
==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.
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==
==Result==


===Relationship between samples in the propestive of hierarchical clustering based on MHL===
===MHL Distrbution in 3 dataaset===


<gallery widths=800px heights=400px>
<gallery widths=800px heights=400px>
File:WGBS.Phase2.Cluster.Revised.3.jpeg|Figure 1A. Hierarchical clustering based on WGBS revealed the relationships between hESC, N37 normals, Salk normals and cancers
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-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>
 
===Relationship between samples in the propestive of hierarchical clustering based on MHL===


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




<gallery widths=800px heights=400px>
File:WGBS.Hclust.Complete.phase2.jpeg|Figure 1A. Hierarchical clustering based on WGBS revealed the relationships between hESC, N37 normals, Salk normals and cancers
</gallery>
</gallery>
*consider: batch differences in read depth, read length or other artifacts.
<gallery widths=800px heights=400px>
<gallery widths=800px heights=400px>
File:RRBS.PhaseI.Cluster.Revise.jpeg|Figure 1B. Hierarchical clustering based on RRBS revealed the relationships between Plasma, Nomal and Cancer tissues.
File:RRBS.PhaseI.Cluster.Revise.jpeg|Figure 1B. Hierarchical clustering based on RRBS revealed the relationships between Plasma, Nomal and Cancer tissues.
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==== Methylation 450K sample with CD, ESC and Cancer sample in the sapce of 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===
====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