Transcript copy number estimation using a mouse whole-genome oligonucleotide microarray

Table 5 Pairwise comparison of expressed transcript sets in developing mouse tissues and cultured cells

Total expressed features	Overlapping features	EM	PL	ES	TS
13,718	EM		9,840	9,212	9,314
10,559	PL			8,508	8,881
9,667	ES				8,816
9,840	TS
Total expressed U-clusters	Overlapping U-clusters	EM	PL	ES	TS
11,360	EM		8,271	7,749	7,853
8,828	PL			7,181	7,492
8,101	ES				7,435
8,271	TS
Total expressed transcripts	Overlapping transcripts	EM	PL	ES	TS
11,762	EM		8,516	7,980	8,090
9,108	PL			7,386	7,718
8,357	ES				7,657
8,534	TS

Sets of microarray features measuring expressed genes (≥ 1 copy per cell) were compared pairwise to calculate the number of members common to each pair. By matching microarray features to the NIA Gene Index, numbers of U-clusters (loci) and transcripts expressed in common were derived for each pairwise comparison. Signal intensities which were lower than those for all spike-in controls, as well as saturated signals, were not converted to copy number estimates (see Materials and methods), so these calculations may underestimate the number of expressed genes.

ISSN: 1474-760X