A comparison of RNA-seq and exon arrays for whole genome transcription profiling of the L5 spinal nerve transection model of neuropathic pain in the rat

Table 2 Total number of genes measurable by RNA-seq and exon arrays at the three probeset confidence levels investigated, for Ensembl ids found in both Rn4 and Rn5 genome builds

Core confidence probesets		RNA-seq:		Totals
Core confidence probesets		Detectable	Not detectable	Totals
Microarray:	Detectable	7153	5	7158
Microarray:	Not detectable	13638	118	13756
	Totals	20791	123	20914
Core and extended confidence probesets		RNA-seq:		Totals
Core and extended confidence probesets		Detectable	Not detectable	Totals
Microarray:	Detectable	13042	13	13055
Microarray:	Not detectable	7749	110	7859
	Totals	20791	123	20914
Core, extended and full confidence probesets		RNA-seq:		Totals
Core, extended and full confidence probesets		Detectable	Not detectable	Totals
Microarray:	Detectable	15492	26	15518
Microarray:	Not detectable	5299	97	5396
	Totals	20791	123	20914

Overlap between genes measurable by either platform, for all core probesets only (top table), core + extended probesets (middle table-the set of probesets used in this study), and core + extended + full probesets (bottom table).

ISSN: 1744-8069