Table 3. Gene ontology (GO) categorization of the 209 differentially expressed plant genes found by SOLiD-SAGE.

	GO Term	Up-regulated genes		Down-regulated genes
		Sequences (n)	%	Sequences (n)	%
1	Autophagy	4	6	0	0
2	Carbohydrate metabolic process	0	0	2	1
3	Cell redox homeostasis	0	0	4	3
4	Cellular carbohydrate metabolic process	0	0	1	1
5	Cellular component organization	3	4	3	2
6	Cellular nitrogen compound metabolic process	2	3	2	1
7	DNA modification	2	3	0	0
8	DNA replication	0	0	1	1
9	Generation of precursor metabolites and energy	1	1	5	4
10	Lipid metabolic process	0	0	7	5
11	Meiosis	1	1	0	0
12	Metabolic process	3	4	2	1
13	Organ senescence	2	3	0	0
14	Oxidation reduction process	1	1	1	1
15	Photosynthesis	9	13	1	1
16	Protein metabolic process	2	3	0	0
17	Protein modification process	4	6	6	4
18	Protein targeting	3	4	3	2
19	Protein ubiquitination	1	1	1	1
20	Regulation of hydrolase activity	2	3	0	0
21	Response to abiotic stimulus	1	1	1	1
22	Response to biotic stimulus	1	1	1	1
23	Response to endogenous stimulus	0	0	1	1
24	Response to metal ion	1	1	1	1
25	Response to stress	8	11	10	7
26	RNA metabolic process	0	0	6	4
27	Signal transduction	2	3	8	6
28	Transcription, DNA-dependent	1	1	5	4
29	Translation	0	0	9	7
30	Transport	6	8	19	14
31	Biological process	3	4	19	14
32	No blastx match found	7	10	9	7
33	No match in NCBI database	2	3	9	7
	Total	72		137

The SAGE tags for each differentially expressed gene can be found in Table S1.