Table 2. Pathway ID and names, total metabolites involved in those pathways, metabolites significantly accumulated in present study and false discovery rate (FDR) in cotton leaves of resistant and susceptible variety, identified by pathway analysis using Arabidopsis thaliana as the pathway library.

ID Annotation	Pathway Annotation	In set	In background	Present in	FDR correction
ath00940	Flavonoid biosynthesis	2	68	SM ST,RT ST, RM SM	5.1
ath00250	Alanine, aspartate and glutamate metabolism	3	24	RT ST, RM RT, SM ST	1.1
ath00910	Nitrogen metabolism	1	26	RM RT, RT ST	1.1
ath00460	Cyanoamino acid metabolism	1	41	SM ST	1.1
ath00564	Glycerophospholipid metabolism	1	46	SM ST	1.1
ath00970	Aminoacyl-tRNA biosynthesis	1	75	RM RT, SM ST	1.4
ath00590	Arachidonic acid metabolism	1	75	SM ST	1.4
ath00480	Glutathione metabolism	4	38	RT ST, SM ST, RM SM, RM RT	1.3
ath001064	Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid	3	67	RT ST	4.0
ath00020	Citrate cycle (TCA cycle)	2	20	RT ST	4.0
ath00710	Carbon fixation in photosynthetic organisms	2	23	RT ST, RM RT	4.3
ath00660	C5-Branched dibasic acid metabolism	2	32	RT ST	4.9
ath00620	Pyruvate metabolism	2	32	RT ST	2.9
ath00944	Flavone and flavonol biosynthesis	2	33	RT ST	4.9
ath00650	Butanoate metabolism	2	40	RT ST	5.9
ath00630	Glyoxylate and dicarboxylate metabolism	2	44	RT ST	6.6
ath0040	Pentose and glucuronate interconversions	2	53	RT ST	7.6
ath00270	Cysteine and methionine metabolism	2	56	RM RT, RT ST	7.6
ath003330	Arginine and proline metabolism	2	82	RT ST, RM RT	1.3
ath00860	Porphyrin and chlorophyll metabolism	3	126	RM RT, RT ST	6.8
ath00340	Histidine metabolism	2	44	RM SM, RM RT	6.9
ath00260	Glycine,serine and Threonne metabolism	2	49	RM RT	7.1
ath01062	Biosynthesis of terpenoids and steroids	2	98	RM SM	1.4