Table 5.

Biological processes with significant genes over-represented after short- and long-term N availability increase

Biological Process	No. in Genome	% in Genome	2 hr N increase			24 hr N increase
			No. in List	% in List	P-value	No. in List	% in List	P-value
Up-regulated
transport	1398	7.7	11	20.4	0.002
cell homeostasis	64	0.4	3	5.6	0.0009
nitrate assimilation	7	0.04	2	3.7	0.0002
sulfate assimilation	11	0.06	2	3.7	0.0005
response to carbohydrate stimulus	29	0.16	2	3.7	0.003
primary metabolism	5170	28.5				203	54.7	1.0E-26
protein biosynthesis	500	2.8				121	32.6	4.2E-98
organelle organization and biogenesis	439	2.4				45	12.1	3.5E-19
ribosome biogenesis and assembly	117	0.6				34	9.2	5.9E-30
translation	136	0.7				13	3.5	4.4E-06
response to auxin stimulus	191	1.1				12	3.2	0.0006
nucleosome assembly	56	0.3				9	2.4	1.8E-06
DNA packaging	106	0.6				9	2.4	0.0003
translational elongation	31	0.2				8	2.2	1.5E-07
nitrogen compound metabolism	124	0.7				8	2.2	0.004
amino acid biosynthesis	99	0.5				7	1.9	0.004
ribonucleotide biosynthesis	45	0.2				5	1.3	0.002
chlorophyll biosynthesis	14	0.08				4	1.1	0.0001
response to cytokinin stimulus	31	0.2	3	5.6	0.0001	4	1.1	0.003
Down-regulated
response to abiotic stimulus	1091	6.0				40	15.5	3.2E-08
secondary metabolism	249	1.4				14	5.4	1.4E-05
response to abscisic acid stimulus	113	0.6				11	4.3	6.3E-07
phenylpropanoid biosynthesis	79	0.4				7	2.7	0.0001
flavonoid biosynthesis	30	0.2				5	1.9	6.0E-05
anthocyanin biosynthesis	8	0.04	1	10	0.004	3	1.2	0.0002
starch biosynthesis	7	0.04				2	0.8	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.