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

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==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==
==Result==


<gallery widths=800px heights=800px>
===MHL Distrbution in 3 dataaset===
File:WGBS.Phase2.Cluster.Revised.jpeg|Figure 1A. Hierarchical clustering based on WGBS revealed the relationships between hESC, N37 normals, Salk normals and cancers
 
<gallery widths=800px heights=400px>
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===
 
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>
*consider: batch differences in read depth, read length or other artifacts.
 
<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.
</gallery>
<gallery widths=800px heights=400px>
File:SeqCap.Phase2.Cluster.Revised.jpeg|Figure 1C.Hierarchical clustering based on SeqCap revealed the relationships between Plasma, Nomal and Cancer tissues.
</gallery>
</gallery>
[[File:RRBS.PhaseI.Cluster.Revise.jpeg|Figure 1B. Hierarchical clustering based on RRBS revealed the relationships between Plasma, Nomal and Cancer tissues.]]
 
[[File:SeqCap.Phase2.Cluster.Revised.jpeg|Figure 1C.Hierarchical clustering based on SeqCap revealed the relationships between Plasma, Nomal and Cancer tissues.]]
===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===
 
====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