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Table 2 Gene ontology (GO) enrichment analysis of genes whose promoter is either hyper- or hypomethylated

From: Oestrogen receptor β regulates epigenetic patterns at specific genomic loci through interaction with thymine DNA glycosylase

GO term p value # Genes (63 in total)
Hypermethylated genes
 Embryonic morphogenesis 4.91E−04 5
 Embryonic appendage morphogenesis 6.39E−04 3
 Embryonic limb morphogenesis 6.39E−04 3
 Regulation of transcription, DNA dependent 7.62E−04 8
 Regulation of RNA metabolic process 8.50E−04 8
 Transcription, DNA dependent 1.01E−03 8
 RNA biosynthetic process 1.03E−03 8
 Appendage morphogenesis 1.12E−03 3
 Limb morphogenesis 1.12E−03 3
 Embryonic development 1.19E−03 6
GO term p value # Genes (223 in total)
Hypomethylated genes
 Developmental process 5.29E−10 52
 Multicellular organismal development 2.70E−09 48
 Anatomical structure development 4.73E−09 44
 System development 1.93E−08 41
 Regulation of transcription from RNA polymerase II promoter 6.70E−08 20
 Regulation of transcription, DNA dependent 7.84E−08 27
 Regulation of RNA metabolic process 1.10E−07 27
 Positive regulation of cellular biosynthetic process 1.42E−07 20
 Transcription from RNA polymerase II promoter 1.66E−07 20
 Transcription, DNA dependent 1.88E−07 27
  1. Included genes show more than 30 % difference in methylation between wt and βerko MEFs, and at least 30 % of all promoter CpGs are covered by more than four reads in both cell types