Whole genome transcriptome polymorphisms in Arabidopsis thaliana

Table 2 The number of significant calls by de novo transcriptome profiling

		Col > Van	Van > Col	Total
Annotation	Differential expression*	1,626	923	2,549
	Differential exonic splicing^†	287	190	477
	Differential intronic splicing^‡	239	220	459
HMM	Differential expression	1,667	1,006	2,673
	Differential splicing	765	457	1,222
	Un-annotated transcript	37	48	85
	Un-annotated 5'	31	32	63
	Un-annotated 3'	30	16	46

*The number of significant calls at a 3% FDR for differentially expressed genes. ^†The number of significant calls for differentially spliced exons using exon probe intensity corrected by gene expression mean. ^‡The number of significant calls at a 3% FDR for differentially spliced introns.

ISSN: 1474-760X