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TCGA-READ: An analysis of methylation alteration and survival rate.

  • Epigenetics
  • Microarray

TCGA-READ: analysis of the methylation alteration and survival rate.

This tutorial is composed of 4 parts.

Part1 '00"00 - A Preparation.

We previously extracted hypo- or hyper-methylated sites from 5 Normal-Tumor pairs. So we import the analyzed data, and also all READ tumor samples. The point is merging platforms before going to the next step.

Part2 '02"50 - Setting Up A Series of All Tumor Samples.

We setup the series to make meaningful visualizations. And we use TCGA sample attributes information to see the effect of those parameters on the survival rate.

Part3 '06"20 - A Clustering Analysis of Hypo- or Hyper-Methylated Sites.

We import the previously defined hypo- and hyper-methylated sites. And then apply clustering of those sites over the all READ tumor samples. We grouped samples into 4 clusters for hypo- sites, and 2 clusters for hyper- sites.

Part4 '10"15 - Kaplan Meier Survival Curve Analysis

We use Kaplan-Meier Survival Curve tool to see the effect of the parameters. Interestingly, it shows hypo-methylated sites do not have clear effect though, hyper-methylated sites may be able to separate samples into good and bad outcomes.

After this analysis, you may want to see the expression profiles of those genes. You can see the RNA-Seq data to examine the effect of expression profiles and survival rate .

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