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Table 7 Top 15 Gene Ontology (GO) categories enriched for genes with DMRs in their promoters

From: Dynamic transcriptome and DNA methylome analyses on longissimus dorsi to identify genes underlying intramuscular fat content in pigs

Category

Term

p-value

Genes

BPa

negative regulation of transcription from RNA polymerase II promoter

2.72E-04

TNF, TRIM29, ANKRD2, CBX4, SMAD3, NFIX, CXXC5, HIC1, LEP, HDAC4, POU5F1, HOXA7, RIPPLY3, SEMA4D, BCOR, ZFHX3, SIM2

BP

negative regulation of myotube differentiation

9.00E-03

HDAC4, PLPP7, ANKRD2

BP

negative regulation of osteoblast differentiation

9.70E-03

HDAC4, TNF, SMAD3, SEMA4D

BP

lipid metabolic process

1.21E-02

FASN, LEP, LCN12, GDPD3, FADS6

CCb

anchored component of plasma membrane

1.21E-02

HYAL2, NTNG1, NTNG2

BP

negative regulation of cell proliferation

1.26E-02

HDAC4, CDKN2B, SMARCB1, IRF6, COPS8, RIPPLY3, FOXO4, CBFA2T3, SIRT2

BP

negative regulation of cell adhesion

1.41E-02

DACT2, PLXNB3, SEMA4D

BP

positive regulation of osteoclast differentiation

1.41E-02

TNF, GNAS, PPARGC1B

BP

ossification

1.64E-02

ALOX15, MGP, EXT2, PPARGC1B

BP

regulation of cell shape

1.67E-02

WASF3, BAIAP2, GNA12, PLXNB3, SEMA4D, ARAP1

MFc

transcription corepressor activity

1.70E-02

HDAC4, SKOR1, POU5F1, BCOR, CBFA2T3, DAXX

BP

embryonic pattern specification

2.02E-02

SMAD3, RIPPLY3, SIM2

MF

sequence-specific DNA binding

2.85E-02

HDAC4, FOXI2, LOC100513063, POU5F1, HOXA7, CXXC5, MAFK, FOXO4, ZFHX3, PITX2

BP

immune response

3.21E-02

FYB, CSF3, CCR7, IL2RA, SMAD3, TGFBR3, VAV1, CCL17

MF

RNA polymerase II transcription factor activity

3.30E-02

FOXI2, LOC100512558, NFIX, FOXO4, NHLH1, SIM2, PITX2

  1. aBP: biological process; bCC: cellular component; cMF: molecular function