Table 2.

Significantly enriched pathways of DEGs in ‘Red Delicious’ and its four generation mutants

Pathway ID	Pathway	Number of DEGs	Enrichment factor	Q-value (<0.05)
	G0 versus G1
ko04626	Plant-pathogen interaction	14	3.97	0.000516177001036455
ko04075	Plant hormone signal transduction	16	3.46	0.000621209033772607
ko00909	Sesquiterpenoid and triterpenoid biosynthesis	4	9.64	0.0409888977775863
	G0 versus G2
ko00941	Flavonoid biosynthesis	16	8.82	1.55373225396715e-09
ko04626	Plant-pathogen interaction	25	3.08	3.9124668653967e-05
ko04712	Circadian rhythm - plant	9	4.96	0.00618212628781434
ko04075	Plant hormone signal transduction	24	2.26	0.0120396678678723
ko00909	Sesquiterpenoid and triterpenoid biosynthesis	6	6.28	0.027494105974142
	G0 versus G3
ko04075	Plant hormone signal transduction	53	2.60	7.99624033653856e-09
ko00941	Flavonoid biosynthesis	15	4.31	0.000139485985032328
ko00909	Sesquiterpenoid and triterpenoid biosynthesis	10	5.46	0.000908007889189655
ko04626	Plant-pathogen interaction	34	2.18	0.00135034354389485
ko04712	Circadian rhythm - plant	12	3.45	0.0158793441067531
ko00900	Terpenoid backbone biosynthesis	12	3.16	0.0371242613055638
	G0 versus G4
ko00196	Photosynthesis - antenna proteins	11	6.29	6.37521150037568e-05
ko04712	Circadian rhythm - plant	15	3.84	0.000640829801345832
ko00941	Flavonoid biosynthesis	15	3.84	0.000640829801345832
ko00900	Terpenoid backbone biosynthesis	15	3.51	0.00196937336544101
ko04075	Plant hormone signal transduction	44	1.92	0.00212458752282485
	G1 versus G2
ko00944	Flavone and flavonol biosynthesis	2	173.44	0.00100183440108559
ko00941	Flavonoid biosynthesis	4	18.26	0.00125854608191001
	G2 versus G3
ko04075	Plant hormone signal transduction	22	3.04	0.000165774159370358
	G3 versus G4
ko04075	Plant hormone signal transduction	16	4.21	4.46200952750608e-05