Table 2

Functional category significance of optimized and marginally significant genes
Functional Category Optimized DESeq marginal edgeR marginal
# of genes p-value # of genes p-value # of genes p-value
Stress 497 0 * 70 2.20E-03 * 19 0.17
Signaling 909 0 * 102 0.43 40 0.70
Cell wall 263 8.51E-29 * 28 0.14 4 0.50
Photosynthesis 117 3.79E-05 * 22 0.76 4 0.23
RNA 1132 6.04E-05 * 222 0.01 * 98 4.40E-03 *
Hormone metabolism 321 3.08E-04 * 36 0.01 * 19 0.51
DNA 133 0.002 * 34 0.70 19 0.03 *
Major CHO metabolism 76 0.003 * 5 0.72 7 0.42
Lipid metabolism 223 0.023 * 23 0.34 16 0.88
Mitochondrial electron transport / ATP synthesis 71 0.042 * 2 0.17 10 0.04 *
TCA cycle 44 0.049 * --- --- 7 0.53

The genes eliminated from Step C in Figure  1 are grouped into functional categories and compared with the final optimized list of significant genes. p-value indicates the significance that transcript abundance of all the genes within a specified category are changing in a similar manner compared to all other categories. 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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