Transcriptome profiling in conifers and the PiceaGenExpress database show patterns of diversification within gene families and interspecific conservation in vascular gene expression

Table 4 Validation of microarray results by RNA-Seq

Criteria		MA¹	RNA-Seq and MA²						RNA-Seq only⁴
P-value	FC (log2)		RPKM > 1		DE³		Tissue pref.		DE	Add
0.05	0.5	5,666	5,592	99%	4,181	75%	4,155	99%	776	19%
0.05	1.0	2,614	2,588	99%	2,265	88%	2,253	99%	677	30%
0.01	0.5	5,526	5,466	99%	3,608	66%	3,585	99%	542	15%
0.01	1.0	2,608	2,582	99%	2,171	84%	2,160	99%	491	23%

¹ DE positive genes determined by MA.
² Number of DE genes detected by RNA-Seq among the DE genes found by MA hybridization; Tissue pref., indicates that the tissue preference for xylem or phelloderm was the same.
³ DE, differential expression in RNA-Seq, determined by a Chi-squared test (df = 1) with Benjamini-Hochberg correction for multiple testing.
⁴ RNA-Seq results for non-DE genes from MA (considering genes represented on the MA only).

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