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Table 1 Gene ontology analysis for differentially methylated sites

From: Depletion of DNMT1 in differentiated human cells highlights key classes of sensitive genes and an interplay with polycomb repression

Type GO FID P OR Ex Obs Total GO Term Grp confirm
Loss
Promoter
 BP 0098609 0.0011 3.0454 4.2148 12 189 Cell–cell adhesion 1 Y
  0007156 0.0011 3.4722 3.0998 10 139 Homophilic cell adhesion via plasma membrane 1 Y
  0010982 0.0015 88.2036 0.0669 2 3 Regulation of high-density lipoprotein particle clearance 2 Y
 MF 0004888 0.0001 1.9709 24.2681 44 1055 Transmembrane signalling receptor activity 3 Y
  0005509 0.0001 2.2488 14.3768 30 625 Calcium ion binding 1 Y
  0004871 0.0003 1.7441 33.6302 54 1462 Signal transducer activity 3 Y
Gene
 BP 0007506 0 130.3775 0.1339 5 7 Gonadal mesoderm development   Y
  0032375 0.0001 25.9783 0.2295 4 12 Negative regulation of cholesterol transport 2 Y
  0045409 0.0001 77.705 0.0956 3 5 Negative regulation of interleukin-6 biosynthetic process 2 Y
 MF 0008083 0.0009 3.5742 3.0015 10 158 Growth factor activity 3 Y
  0004984 0.0014 2.5939 6.136 15 323 Olfactory receptor activity 3 Y
  0038023 0.0014 1.7776 22.9102 38 1206 Signalling receptor activity 3 Y
Gain
Promoter
 BP 0035574 0 443.1106 0.4729 14 15 Histone H4-K20 demethylation 4 N
  0045653 0 147.6833 0.5359 14 17 Negative regulation of megakaryocyte differentiation   N
  0016577 0 26.4022 1.0404 15 33 Histone demethylation 4 N
 MF 0035575 0 452.3692 0.4637 14 15 Histone demethylase activity (H4-K20 specific) 4 N
  0032451 0 21.0879 1.1747 15 38 Demethylase activity 4 N
  0015020 0 10.1109 0.8965 7 29 Glucuronosyltransferase activity   Y
Gene
 BP 0035574 0 280.0725 0.4039 14 16 Histone H4-K20 demethylation 4 N
  0045653 0 140.0181 0.4544 14 18 Negative regulation of megakaryocyte differentiation   N
  0006335 0 31.0869 0.8078 14 32 DNA replication-dependent nucleosome assembly 4 N
 MF 0035575 0 287.2955 0.3942 14 16 Histone demethylase activity (H4-K20 specific) 4 N
  0032451 0 24.654 0.9856 15 40 Demethylase activity 4 N
  0004984 0 4.4768 7.9586 31 323 Olfactory receptor activity 3 Y
  1. BP biological process, MF molecular function, GO FID gene ontology family identification code, P probability value, OR odds ratio, Ex expected number of hits, Obs observed number, Total total number of genes in that family, Grp-see below; confirm Y/N, confirmation given by FDR tracks Yes/No
  2. Groups (Grp): 1 = neuroepithelium; 2 = Fat homoeostasis/body mass (FBM); 3 = olfactory receptor; 4 = histone modifier