Table 3.

The most reliable top ten significantly enriched pathways of DEGs in the three differential expression gene sets.

DEF-Sets	Pathway ID	Pathway	DEGs in Pathway	All Genesin Pathway	p-Value
A_B	ko00196	Photosynthesis—antenna proteins	10	30	9.95 × 10−7
	ko00941	Flavonoid biosynthesis	11	48	1.68 × 10−5
	ko00130	Ubiquinone and other terpenoid–quinone biosynthesis	11	59	0.000127
	ko00195	Photosynthesis	13	86	0.00029
	ko00360	Phenylalanine metabolism	12	76	0.000327
	ko00940	Phenylpropanoid biosynthesis	20	184	0.000769
	ko04075	Plant hormone signal transduction	26	271	0.000916
	ko00052	Galactose metabolism	13	107	0.002352
	ko00945	Stilbenoid, diarylheptanoid, and gingerol biosynthesis	5	20	0.002448
	ko00350	Tyrosine metabolism	10	72	0.002749
A_C	ko00196	Photosynthesis—antenna proteins	15	30	6.93 × 10−10
	ko00500	Starch and sucrose metabolism	44	281	2.45 × 10−6
	ko04075	Plant hormone signal transduction	40	271	2.95 × 10−5
	ko04070	Phosphatidylinositol signaling system	16	103	0.004376
	ko00940	Phenylpropanoid biosynthesis	24	184	0.005951
	ko00350	Tyrosine metabolism	12	72	0.007305
	ko00460	Cyanoamino acid metabolism	12	72	0.007305
	ko04712	Circadian rhythm—plant	12	74	0.00909
	ko00360	Phenylalanine metabolism	12	76	0.011198
	ko00960	Tropane, piperidine, and pyridine alkaloid biosynthesis	8	42	0.012192
B_C	ko03010	Ribosome	35	635	5.29 × 10−5
	ko00500	Starch and sucrose metabolism	19	281	0.000262
	ko00941	Flavonoid biosynthesis	7	48	0.000307
	ko00052	Galactose metabolism	9	107	0.002673
	ko00196	Photosynthesis—antenna proteins	4	30	0.008731
	ko00940	Phenylpropanoid biosynthesis	11	184	0.012611
	ko04626	Plant–pathogen interaction	14	262	0.01331
	ko00945	Stilbenoid, diarylheptanoid, and gingerol biosynthesis	3	20	0.016597
	ko00520	Amino sugar and nucleotide sugar metabolism	11	213	0.033104
	ko00905	Brassinosteroid biosynthesis	2	14	0.055219