Ns126:Calendar/NOTES/2015-6-12: Difference between revisions

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*heatmap based on DMR and DMRs in CpG Shore region (Figuare 1c,1d,1e and 1f)
*heatmap based on DMR and DMRs in CpG Shore region (Figuare 1c,1d,1e and 1f)


*Dendrogram based on genome-wide DNA methylation for human can be found here [[File:Figure1.dendrogram.euclidean.ward.hclust.pdf]]


*For human ips and SCNT data, the methylation status of 4377908 CpG were shared by 11 samples(2 ES, 1 Fibroblast, 4 ips and 4 SCNT). PCA analysis based on the genome-wide DNA methylation data showed the first and second principle component can explain almost 50% variances. In the dimension of first component fibroblast were obviously separated with ES,ips and SCNT. In the dimension of the second component, ES was separated with ips and SCNT with clear boundary.
*For human ips and SCNT data, the methylation status of 4377908 CpG were shared by 11 samples(2 ES, 1 Fibroblast, 4 ips and 4 SCNT). PCA analysis based on the genome-wide DNA methylation data showed the first and second principle component can explain almost 50% variances. In the dimension of first component fibroblast were obviously separated with ES,ips and SCNT. In the dimension of the second component, ES was separated with ips and SCNT with clear boundary.

Revision as of 21:48, 12 June 2015

Today's task:

  • Merge genome-wide DNA methylation data of human and mice
  • Dendrogram based on genome-wide DNA methylation data(Figure 1a and 1b)
  • heatmap based on DMR and DMRs in CpG Shore region (Figuare 1c,1d,1e and 1f)


  • For human ips and SCNT data, the methylation status of 4377908 CpG were shared by 11 samples(2 ES, 1 Fibroblast, 4 ips and 4 SCNT). PCA analysis based on the genome-wide DNA methylation data showed the first and second principle component can explain almost 50% variances. In the dimension of first component fibroblast were obviously separated with ES,ips and SCNT. In the dimension of the second component, ES was separated with ips and SCNT with clear boundary.