Table 4.

Significant enriched pathways in SAP1-VS-SAP2 paired comparison of Rubus.

No.	Pathway	DEGs genes with pathway annotation (6157)	All genes with pathway annotation (32310)	P-value	Q-value	Pathway ID	Level 1	Level 2
1	Flavonoid biosynthesis	96 (1.56%)	237 (0.73%)	1.60E-14	2.14E-12	ko00941	Metabolism	Biosynthesis of other secondary metabolites
2	Circadian rhythm - plant	94 (1.53%)	269 (0.83%)	5.29E-10	3.54E-08	ko04712	Organismal Systems	Environmental adaptation
3	Biosynthesis of secondary metabolites	916 (14.88%)	4123 (12.76%)	2.93E-08	1.31E-06	ko01110	Metabolism	Global and overview maps
4	Stilbenoid, diarylheptanoid and gingerol biosynthesis	81 (1.32%)	242 (0.75%)	6.96E-08	2.33E-06	ko00945	Metabolism	Biosynthesis of other secondary metabolites
5	Cyanoamino acid metabolism	105 (1.71%)	349 (1.08%)	4.28E-07	1.15E-05	ko00460	Metabolism	Metabolism of other amino acids
6	Sesquiterpenoid and triterpenoid biosynthesis	40 (0.65%)	105 (0.32%)	4.16E-06	9.30E-05	ko00909	Metabolism	Metabolism of terpenoids and polyketides
7	Porphyrin and chlorophyll metabolism	68 (1.1%)	213 (0.66%)	4.87E-06	9.33E-05	ko00860	Metabolism	Metabolism of cofactors and vitamins
8	Photosynthesis - antenna proteins	18 (0.29%)	36 (0.11%)	2.80E-05	4.69E-04	ko00196	Metabolism	Energy metabolism
9	Limonene and pinene degradation	48 (0.78%)	146 (0.45%)	4.95E-05	7.37E-04	ko00903	Metabolism	Metabolism of terpenoids and polyketides
10	Plant hormone signal transduction	251 (4.08%)	1074 (3.32%)	0.000201	2.69E-03	ko04075	Environmental Information Processing	Signal transduction
11	Phenylpropanoid biosynthesis	194 (3.15%)	813 (2.52%)	0.000336	4.10E-03	ko00940	Metabolism	Biosynthesis of other secondary metabolites
12	Ascorbate and aldarate metabolism	59 (0.96%)	212 (0.66%)	0.001173	1.31E-02	ko00053	Metabolism	Carbohydrate metabolism