Table 3

Statistical limitations are revealed by independent analysis of ozone-responsive genes
Functional annotation Locus ID Transcript length Control RPKM Treatment RPKM Fold change DESeq edgeR Individual t-test
Light-harvesting complex II CAB protein Glyma05g25810 1100 7733.20 ± 783.0 4575.86 ± 429.3 0.59 0.063 3.39E-04 * 0.004 *
Ubiquitin Glyma20g27950 1540 1504.18 ± 149.8 2425.15 ± 206.1 1.61 0.061 0.007 * 0.003 *
Thioredoxin Glyma17g37280 1134 265.49 ± 11.1 220.79 ± 17.8 0.83 0.14 0.213 0.021 *
L-ascorbate peroxidase Glyma11g11460 1278 84.73 ± 2.6 107.98 ± 4.4 1.27 0.214 0.272 0.001 *
Polysaccharide catabolism Glyma06g45700 1831 70.47 ± 8.6 18.91 ± 9.2 0.27 2.34E-29 * 4.48E-19 * 0.002 *
Glutaredoxin Glyma13g30770 747 11.31 ± 1.4 34.68 ± 6.8 3.07 8.39E-14 * 1.56E-11 * 0.004 *
Protein degradation DER1 like Glyma04g14250 1088 5.23 ± 0.2 44.52 ± 11.8 8.51 7.06E-49 * 8.30E-38 * 0.005 *
Lipoxygenase Glyma03g42500 2833 2.90 ± 0.4 5.64 ± 1.3 1.95 1.96E-04 * 2.26E-04 * 0.027 *
Starch synthase catalytic domain Glyma20g36040 1954 2.84 ± 0.8 0.12 ± 0.1 0.04 1.14E-23 * 1.60E-36 * 0.005 *
WRKY trascription factor Glyma10g27860 1468 1.69 ± 0.4 70.92 ± 20.80 41.97 9.23E-121 * 2.76E-92 * 0.005 *

Genes known to be regulated by elevated ozone that had a range of transcript abundances were selected from the optimized list of differentially regulated genes. In addition to p-values from DESeq and edgeR, an ANOVA was performed on RPKM values. Asterisks signify p-value below p = 0.05.

Yendrek et al.

Yendrek et al. BMC Research Notes 2012 5:506   doi:10.1186/1756-0500-5-506

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