An integrated gene annotation and transcriptional profiling approach towards the full gene content of the Drosophila genome

Table 3 Summary for the Heidelberg Collection R2

	Total	Heidelberg Predictions	FlyBase Release 3.1	Other	Common predictions
Heidelberg Collection R2	19,879	6,224	605	nd	13,050
Heidelberg PrimerSet	19,095 (19,389)	6,224 (294)	296	40	12,535
Heidelberg FlyArray	18,837 (19,123)	6,143 (286)	288	39	12,367
Expressed during development	12,574 (66.8%) (12,734) (66.6%)	2,636 (42.9%) (160) (55.9%)	167 (57.9%)	30 (76.9%)	9,741 (78.8%)
Validation by RT-PCR	354/438 (80.8%)	218/293 (74.4%)	ND	ND	136/145 (93.8%)

The Heidelberg Collection R2 resulted from the combination of our novel annotation with the recently published FlyBase Release 3.1 annotation (excluding non-CG annotations, such as TE and CR). Only Heidelberg Predictions, primers and amplicons that matched with high stringency to the FlyBase genomic sequence Release 3.1 were included and re-assigned to the new Heidelberg Collection R2, thus all numbers represent a lower limit. Moreover, numbers in the table are corrected for several amplicons matching a single gene. As before, the PrimerSet includes all annotations for which we successfully designed primer pairs, and likewise, the Heidelberg FlyArray sums up the annotations that are included on the microarray. The next row presents the results of the developmental profiling; numbers given in parentheses are the percentage of annotations represented on the array that scored positive. The last row shows the validation rate of the microarray results by RT-PCR (amplicon length ≤750 bp). In the column for the Heidelberg Predictions we included below (in parentheses) the number of annotations that were unique to BDGP Release 2 and are not part of the FlyBase Release 3.1 CG annotations.

ISSN: 1474-760X