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.