Table 4.

Biological processes with significant genes over-represented under mild or severe chromic N stress

Biological Process	No. in Genome	% in Genome	Under mild N stress			Under severe N stress
			No. in List	% in List	P-value	No. in List	% in List	P-value
Up-regulated
response to abiotic stimulus	1091	6.0	16	40	4.2E-10	39	19.3	7.3E-11
response to stress	945	5.2	14	35	6.4E-09	23	11.4	0.0004
secondary metabolism	249	1.4	6	15	1.6E-05	15	7.4	1.3E-07
response to oxidative stress	140	0.8	5	12.5	1.4E-05	8	4.0	0.0002
flavonoid biosynthesis	30	0.2	2	5	0.002	6	3.0	8.4E-07
anthocyanin biosynthesis	8	0.04	2	5	0.007	3	1.5	7.3E-05
phenylpropanoid biosynthesis	79	0.4				9	4.5	2.3E-07
response to abscisic acid stimulus	113	0.6				9	4.5	4.8E-06
organ senescence	12	0.07				3	1.5	0.0003
starch biosynthesis	7	0.04				2	1.0	0.002
Down-regulated
primary metabolism	5170	28.5				58	43.0	0.0002
biosynthesis	1269	7.0				28	20.7	1.6E-07
protein biosynthesis	500	2.8				17	12.6	1.9E-07
response to auxin stimulus	191	1.1				10	7.4	1.7E-06
generation of precursor metabolites and energy	451	2.5				10	7.4	0.002
nitrogen compound metabolism	276	1.5				7	5.2	0.005
response to cytokinin stimulus	31	0.2				5	3.7	3.1E-06
main pathways of carbohydrate metabolism	95	0.5				4	3.0	0.006
photosynthesis	44	0.2				3	2.2	0.004

The gene list was imported into GeneSpring. The number of genes in each biological process either in a whole genome (No. in Genome), or in the list (No. in list), as well as their corresponding percentage and p-value was generated by GeneSpring.