Table 13.

The comparison results of signature selection and differential variant analysis.

Categories	Gene name	Description	SSA	DVA
DNA repair	MMS22L	DNA repair protein	*
	PRIM2	DNA primase	*
	MRE11A	Double-strand break repair protein	*
	DNASE2	Deoxyribonuclease-2-beta precursor	*
	DDIAS	Induced by UV radiation. DNA damage-induced apoptosis suppressor	*
	DCLRE1A	5′-3′ exodeoxyribonuclease activity		*
	TATDN1	Deoxyribonuclease activity		*
	DCLRE1A	Double-strand break repair		*
	COBLL1	DNA biosynthetic process		*
	POLQ	Double-strand break repair		*
	PRKDC	DNA repair		*
	DCLRE1A	Inter strand cross-link repair		*
Immune response	TRAT1	T cell receptor associated transmembrane adaptor 1	*	*
	BMX	BMX non-receptor tyrosine kinase	*
	BMX	NK T cell differentiation		*
	CXCR4	C-X-C chemokine receptor type 4	*
Organ development	BDNF	Brain-derived neurotrophic factor	*
	LRP6	Cerebral cortex development		*
	LRP6	Midbrain development		*
	LRP6	Thalamus development		*
Mitochondrion function (cell respiration)	COX7A2	Cytochrome c oxidase subunit 7A2	*
	MTO1	Protein MTO1 homolog, mitochondrial	*
	ME3	Malic enzyme 3, mitochondrial	*
	DARS2	aspartyl-tRNA synthetase 2, mitochondrial	*
	PRELID1	PRELI domain-containing protein 1, mitochondrial	*
	TIMM10	Translocase of inner mitochondrial membrane	*
	MRPS11	28S ribosomal protein S11, mitochondrial	*
	MRPL46	39S ribosomal protein L46, mitochondrial	*
	MELANOMA	Gallus gallus mitochondrial ribosomal nuclear gene encoding mitochondrial protein	*
	DLD	dihydrolipoyl dehydrogenase, mitochondrial	*
	MICU3	Mitochondrial calcium uptake family ember 3	*
	HCCS	Cytochrome c-type hemelyase	*
	UQCRC1	Mitochondrial electron transport		*
	UQCRC1	Mitochondrial respiratory chain complex III		*
Epigenetic regulation	ATAD2	Histone binding		*
	SERPINB10	Heterochromatin-associated protein MENT. Chromatin DNA binding	*
Protein hemostasis	PSMD13	Proteasome accessory complex		*
	PSMD13	Proteasome regulatory particle		*
	PSMD13	Proteasome assembly		*
	PSMG3	Proteasome assembly chaperone 3	*

The comparable results were obtained by signature selection and differential variants analysis. The results of differential variants analysis indicated that adaptive variants were involved in DNA repair, organs development, immune response, epigenetic regulation, mitochondrion function (cell respiration) and protein hemostasis. Interestingly, the similar results were reported by signature selection analysis and it is recognized that both analysis show the similar gene’s functions that contribute in response to hypoxia. SSA: signature selection analysis. DVA: differential variant analysis.