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

Table 2 Dataset for evaluating tag assignment

Dataset	Subset	Total	w/o Tags^a	w/Tags	Hits^b	%
cDNA	cDNA	2480	0	2480	2480	100
Unigene^c	Unigene	2806	3	2803	2627	93.62
	Uni-S	2712	1	2711	2598	95.80
	Uni-N	94	1	93	29	30.85
	UniBest	2480	0	2480	2414	97.34
	Max-Length	2480	0	2480	2411	97.22
EST^c	EST	54764	3597	51167	36484	66.62
	EST-S	26242	1631	24611	18788	71.60
	EST-A	2749	182	2567	1665	60.57
	EST-N	21169	1592	19577	12702	60.00
	EST-B	4604	192	4412	3329	72.31
	ESTBest	2480	19	2461	1842	74.27
	Max-Length	2480	19	2461	1858	74.92
Predicted^d	Predicted	2480	44	2436	415	16.73
	P-100	2480	26	2454	787	31.73
	P-200	2480	9	2471	1308	52.74
	P-300	2480	4	2476	1457	58.75
	P-400	2480	2	2478	1181	47.62
	P-500	2480	1	2479	869	35.04

^a Numbers of cDNA sequences that do not have tags due to the absence of NlaIII sites. ^b Numbers of virtual tags that matched to our empirical dataset. ^c Capital letters stand for transcripts that have 3' polyA signal (S), 3' polyA tail (A), both the signal and the tail (B), and neither (N), respectively. ^d Predicated gene models and extended lengths (bp) from stop codon (P-100 to P-500).

ISSN: 1471-2229