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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
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Epigenetics & Chromatin

ISSN: 1756-8935