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Table 4 Validation of microarray results by RNA-Seq

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

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. 1 DE positive genes determined by MA.
  2. 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. 3 DE, differential expression in RNA-Seq, determined by a Chi-squared test (df = 1) with Benjamini-Hochberg correction for multiple testing.
  4. 4 RNA-Seq results for non-DE genes from MA (considering genes represented on the MA only).
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