Dinh 2011/NOTES/2011-7-8: Difference between revisions

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# Finally, a list of all gene-cg interactions involved in either glycolysis, oxidative phosphorylation, or citrate cycle.  
# Finally, a list of all gene-cg interactions involved in either glycolysis, oxidative phosphorylation, or citrate cycle.  
  [[File:Example.jpg | Glycolysis matrix ]]
  [[File:file | Glycolysis matrix ]]
  [[File:Example.jpg | Oxidative phosphorylation matrix]]
  [[File:file | Oxidative phosphorylation matrix]]
  [[File:Example.jpg | TCA cycle matrix]]
  [[File:file | TCA cycle matrix]]

Revision as of 20:27, 9 July 2011

Correlation of DNA methylation with reprogramming efficiency and metabolic genes

Athanasia have found that the reprogramming efficiencies of different somatic cell types may be due to their differential use of metabolic pathways especially oxidative phosphorylation and glycolysis. Her study mainly focused on comparing Keratinocytes and fibroblasts with the addition of HUVECs. Although we did not used cells of the same lineages, we have methylation data for these cell types.

The question from reviewers were concerning whether we see differential methylation patterns associated with the genes involved in either of these pathways

The following analysis was done using the BSPP data for 
K-MMTA, KiPS4F8, HFF-XF, FiPS3F1, FiPS4F7, HUVEC, HUViPS4F1, HUViPS4F3, H1, and H9.
  1. First, I did paired-wise calculation of DMS using Benjamini Hochberg's FDR 0.01. Only the sites available between pairs at 10x coverage were considered. Finally, I merged all DMSs together, and obtained a set of "potential" DMSs
  1. I uploaded the "potential" DMSs to GREAT, and obtained a list of possible Gene-CG site interactions.
  1. Next, I went to KEGG and downloaded the genes involved in oxidative phosphorylation, glycolysis, and then in the citrate cycle.
  1. Crossed the potential genes-cg interaction list with the gene list in each pathways
Note: A CG site may have interaction with more than one gene, but not likely in the same pathway we are looking at.
  1. Finally, a list of all gene-cg interactions involved in either glycolysis, oxidative phosphorylation, or citrate cycle.
Glycolysis matrix
Oxidative phosphorylation matrix
TCA cycle matrix