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.

Zhang et al. Genome Biology 2008 9:R165   doi:10.1186/gb-2008-9-11-r165