Table 1. Gene Ontology analysis of differentially methylated genes.
| GO ID | GO term | No. of Genes | Log2 Difference | P-value | Top 10 genes in each GO |
| ES cells vs. pMEFs comparison (pMEF-ES) | |||||
| GO:0005634 | Nucleus | 762 | 0.0827 | 5.15E-11 | Nanog, Ihpk1, Thap1, Mrps31, Mafg, Mapk14, Grwd1, Pml, Nicn1, Tceb2 |
| GO:0008270 | Zinc ion binding | 371 | 0.0808 | 2.96E-04 | Thap1, Pam, Rasa2, Mpi1, Pml, Rnf2, Zfp60, Zfp113, Aebp2, Zcchc9 |
| GO:0043687 | Post-translational protein modification | 289 | 0.0897 | 3.66E-04 | Mapk14, Map1lc3a, Tceb2, Rnf2, Tnk1, Arih2, Npr1, Ern1, Cln3, Ece2 |
| GO:0006355 | Regulation of transcription, DNA-dependent | 445 | 0.0647 | 8.89E-03 | Nanog, Mrps31, Mafg, Mapk14, Pml, Tceb2, Rnf2, Zfp60, Zfp113, Aebp2 |
| GO:0006512 | Ubiquitin cycle | 77 | 0.1545 | 1.93E-02 | Map1lc3a, Tceb2, Rnf2, Arih2, Ube2i, Ube4a, Fbxo15, Ppil2, Usp18, Wwp2 |
| ES cells vs. TS cells comparison (TS-ES) | |||||
| GO:0005634 | Nucleus | 763 | 0.0514 | 1.00E-15 | Ihpk1, Mrps31, Thap1, Nicn1, Mafg, Zfp426, Banp, Zfp239, Rragc, Msh4 |
| GO:0006355 | Regulation of transcription, DNA-dependent | 445 | 0.0453 | 8.20E-05 | Mrps31, Mafg, Zfp426, Zfp239, Ankfy1, Mapk14, Nanog, Ankrd6, Snapc3, Zfp60 |
| GO:0006396 | RNA processing | 68 | 0.0931 | 2.70E-03 | Rragc, Ern1, Rpp30, Frg1, Papd1, Ddx56, Trit1, Sf3b1, Rg9mtd3, Nol3 |
| GO:0008270 | Zinc ion binding | 371 | 0.0403 | 9.20E-03 | Pam, Thap1, Kcmf1, Zfp426, Zfp239, Ankfy1, Zfp60, Rasa2, Zfp113, Zfp84 |
Comparisons were made between ES cells versus pMEFs and ES cells versus TS cells to establish within which GO categories the promoter methylation was most changing. The data used for the GO analysis were the subtracted average log2 ratios from two tissues for the 900 bp upstream of genes on autosomal chromosomes. Only promoters with a CpG content of 2–9% and which contained at least 5 probes were used. Interesting categories were judged to be those with p-value of <0.01. Where multiple nested categories were present only the most specific category (the one with the highest GO level) was kept. Genes within each category were ordered by the significance of difference in promoter methylation between the two cell types and the top 10 genes are shown as examples-these were all found to be hypomethylated in ES cells and hypermethylated in pMEFs or TS cells respectively.