TABLE 3.

GO terms enriched in the genes that showed differential expression accompanied by altered DNA methylation in male (A) and female (B) offspring in the TiO₂-H group.

A
ID	GO term	Enrichment factor	p-value
GO:0005923	Bicellular tight junction	8.99	<0.001
GO:0015629	Actin cytoskeleton	5.07	0.003
GO:0003779	Actin binding	3.28	0.018
GO:0008285	Negative regulation of cell population proliferation	3.07	0.024
GO:0045893	Positive regulation of transcription, DNA-templated	2.71	0.014
GO:0007275	Multicellular organism development	2.63	0.001
GO:0003700	DNA-binding transcription factor activity	2.63	0.017
GO:0043565	Sequence-specific DNA binding	2.50	0.033
GO:0030054	Cell junction	2.42	0.012
GO:0006355	Regulation of transcription, DNA-templated	2.34	0.010
GO:0000981	DNA-binding transcription factor activity, RNA polymerase II-specific	2.14	0.038
GO:0045944	Positive regulation of transcription by RNA polymerase II	2.08	0.029

B
ID	GO term	Enrichment factor	p-value
GO:0031175	Neuron projection development	6.05	0.001
GO:0010468	Regulation of gene expression	5.20	<0.001
GO:0003700	DNA-binding transcription factor activity	5.01	<0.001
GO:0005667	Transcription regulator complex	4.94	<0.001
GO:0001228	DNA-binding transcription activator activity, RNA polymerase II-specific	4.86	<0.001
GO:1990837	Sequence-specific double-stranded DNA binding	4.71	<0.001
GO:0000977	RNA polymerase II transcription regulatory region sequence-specific DNA binding	4.67	<0.001
GO:0043565	Sequence-specific DNA binding	4.17	<0.001
GO:0031625	Ubiquitin protein ligase binding	3.97	0.004
GO:0008134	Transcription factor binding	3.91	0.002
GO:0045893	Positive regulation of transcription, DNA-templated	3.88	<0.001
GO:0007283	Spermatogenesis	3.79	0.001
GO:0045892	Negative regulation of transcription, DNA-templated	3.70	<0.001
GO:0016604	Nuclear body	3.69	0.005
GO:0045944	Positive regulation of transcription by RNA polymerase II	3.65	<0.001
GO:0008285	Negative regulation of cell population proliferation	3.58	0.003
GO:0007275	Multicellular organism development	3.48	<0.001
GO:0000978	RNA polymerase II cis-regulatory region sequence-specific DNA binding	3.47	<0.001
GO:0000981	DNA-binding transcription factor activity, RNA polymerase II-specific	3.38	<0.001
GO:0006357	Regulation of transcription by RNA polymerase II	3.36	<0.001
GO:0006355	Regulation of transcription, DNA-templated	3.31	<0.001
GO:0001701	In utero embryonic development	3.18	0.021
GO:0000122	Negative regulation of transcription by RNA polymerase II	2.97	<0.001
GO:0008270	Zinc ion binding	2.93	0.002
GO:0019899	Enzyme binding	2.82	0.020
GO:0043065	Positive regulation of apoptotic process	2.80	0.033
GO:0003677	DNA binding	2.80	0.000
GO:0030424	Axon	2.74	0.022
GO:0003779	Actin binding	2.73	0.036
GO:0010628	Positive regulation of gene expression	2.69	0.015
GO:0016491	Oxidoreductase activity	2.68	0.010
GO:0042803	Protein homodimerization activity	2.68	0.006
GO:0030154	Cell differentiation	2.66	0.001
GO:0019901	Protein kinase binding	2.62	0.018
GO:0042995	Cell projection	2.53	0.001
GO:0005694	Chromosome	2.43	0.037
GO:0045202	Synapse	2.39	0.013
GO:0030054	Cell junction	2.24	0.014
GO:0031410	Cytoplasmic vesicle	2.21	0.021

The enrichment factor for each category was defined as described in Materials and Methods. Statistical analysis was performed using Fisher’s exact test with hypergeometric distribution and the level of statistical significance was set at p < 0.05.