Comparative expression profiling in grape (Vitis vinifera) berries derived from frequency analysis of ESTs and MPSS signatures

Table 2 Distinct MPSS signatures matching EST contigs or singletons classified based on "reliability" and "significance" filters.

	Significant	Non-significant
A. Filter results for 11,345 17-base signatures matching EST contigs.
	8,012 (66.2%)	4,094 (33.8%)
Reliable	7,686 (63.5%)	1,734 (14.3%)
9,420 (77.8%)	6,519 contigs	1,235 contigs
Non-reliable	326 (2.7%)	2,360 (19.5%)
2,686 (22.2%)	632 contigs	2,276 contigs
B. Filter results for 10,179 20-base signatures matching EST contigs.
	Significant	Non-significant
	7,053 (65.3%)	3,751 (34.7%)
Reliable	6,698 (61.1%)	1,473 (13.6%)
8,171 (75.6%)	5,830 contigs	1,490 contigs
Non-reliable	355 (3.3%)	2,278 (21.1%)
2,633 (24.4%)	386 contigs	2,155 contigs
C. Filter results for 3,889 17-base signatures matching EST singletons.
	Significant	Non-significant
	2,700 (64.6%)	1,477 (35.4%)
Reliable	2,587 (61.9%)	638 (15.3%)
3,225 (77.2%)	2,423 singletons	663 singletons
Non-reliable	113 (2.7%)	839 (20.1%)
952 (22.8%)	127 singletons	857 singletons
D. Filter results for 3,367 20-base signatures matching EST singletons.
	Significant	Non-significant
	2,318 (64.4%)	1,282 (35.6%)
Reliable	2,207 (61.3%)	499 (13.9%)
2,706 (75.2%)	2,096 singletons	511 singletons
Non-reliable	111 (3.1%)	783 (21.8%)
894 (24.8%)	128 singletons	780 singletons

Percentages refer to the total distinct signatures. Filters are described in the text, and are as defined in Meyers et al., [11]. In parts A and B, the number of EST contigs matched was out of a total of 6,430 unique contigs matched by 17-base signatures or 5,831 by 20-base signatures; signatures from different filter categories may match to the same contig (see Additional file 1A–1B and Table 3 for details). In parts C and D, the number of EST singletons matched was out of a total of 2,190 unique singletons matched by 17-base signatures or 2,097 by 20-base signatures; signatures from different filter categories may match to the same singleton (see Additional file 1A–1B and Table 3 for details).

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