Differential gene expression in an elite hybrid rice cultivar (Oryza sativa, L) and its parental lines based on SAGE data

Song, Shuhui; Qu, Hongzhu; Chen, Chen; Hu, Songnian; Yu, Jun

doi:10.1186/1471-2229-7-49

Table 5 Differentially-expressed genes from 93-11 leaf libraries confirmed by microarray data

From: Differential gene expression in an elite hybrid rice cultivar (Oryza sativa, L) and its parental lines based on SAGE data

Gene Model	Tag	Tag Number			Ratio^b	Microarray Signal			Annotations
		N^a	P^a	L^a		N^a	P^a	L^a
Up-Regulated Tags (≥2-fold)
9311_Chr08_2156	GATTTGTATA	1	0	33	66.00	251	200	275	Plastocyanin-like
9311_Chr06_1523	TCATTTCAGT	2	0	14	14.00	3706	3473	6017	Major intrinsic protein
9311_Chr06_1142	ATCTGTTGCT	0	2	8	8.00	224	246	263	EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase)
9311_Chr07_1712	GATCCGTCTC	13	0	47	7.23	1288	1238	2097	Thiamine biosynthesis Thi4 protein
9311_Chr06_1545	GTACTGTCTG	13	19	55	3.44	249	361	410	Ubiquitin
9311_Chr03_1401	TTCCCCCATT	11	4	22	2.93	261	150	263	Protein of unknown function DUF250
9311_Chr05_0842	CTGTATTACT	41	47	94	2.14	1030	994	1072	Calcium-binding EF-hand
Down-Regulated Tags (>2-fold)
9311_Chr11_0807	GAATATTGGA	0	43	3	7.17	854	1030	976	Sucrose synthase
9311_Chr10_2185	TATCATTACA	40	169	19	5.50	2536	3225	1968	Mitochondrial substrate carrier
9311_Chr07_1231	CACATAAATT	38	26	6	5.33	3539	1750	957	Photosystem I reaction centre subunit IV/PsaE
9311_Chr03_0009	TACATAGACA	23	66	11	4.05	667	681	659	Unknown
9311_Chr03_3682	ATTGCGGAAT	103	323	55	3.87	4577	5270	3054	Glycine hydroxymethyl transferase
9311_Chr01_4972	GATCGATGGG	4	53	8	3.56	239	747	504	Cellular retinaldehyde-binding)/triple function, C-terminal
9311_Chr03_3625	ACACTACAGT	2	36	6	3.17	203	401	245	Unknown
9311_Chr03_4144	CTTACAAGTG	25	58	14	2.96	929	947	655	Rieske [2Fe-2S] region
9311_Chr01_2088	GAGAGAGGGA	117	186	52	2.91	6807	7259	3098	Photosystem II manganese-stabilizing protein PsbO
9311_Chr12_1000	GATATATGGA	69	256	58	2.80	2501	2801	1201	Photosystem I reaction centre, subunit XI PsaL
9311_Chr04_3185	TAGTGATAAG	8	36	8	2.75	1563	1689	1217	Lipase, class 3
9311_Chr03_0940	ATCGCCGAGA	19	68	17	2.56	1520	2064	1220	Glutamine synthetase, beta-Grasp
9311_Chr01_4844	GTTAGCAAAA	11	17	6	2.33	2280	2985	1878	Calsequestrin
9311_Chr06_2649	AGGGAGGCCG	25	2	6	2.25	246	192	222	Heat shock protein DnaJ, N-terminal

^a P, N, and L stand for PA64s, 9311, and LYP9, respectively. ^b Ratios are calculated as ratio = L/[(P+N)/2] for up-regulated tags and [(P+N)/2]/L for down-regulated tags.

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ISSN: 1471-2229

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