Table 2.
Significantly regulated biological processes (FDR < 0.05) which are commonly regulated in at least 6 of 9 transcriptomic studies
| GO_ID | GO_TERM | Count | P-value | Benjamini test |
|---|---|---|---|---|
| DOWN-REGULATED | ||||
| GO:0006633 | fatty acid biosynthetic process | 3 | 7.02E-250 | 5.80E-247 |
| GO:0015031 | protein transport | 6 | 2.93E-129 | 1.21E-126 |
| GO:0016192 | vesicle-mediated transport | 4 | 1.08E-117 | 2.96E-115 |
| GO:0046777 | protein autophosphorylation | 5 | 3.73E-117 | 7.70E-115 |
| GO:0006468 | protein phosphorylation | 13 | 4.54E-32 | 7.49E-30 |
| GO:0006839 | mitochondrial transport | 3 | 8.95E-26 | 1.23E-23 |
| GO:0006096 | glycolytic process | 3 | 1.83E-23 | 2.16E-21 |
| GO:0006412 | Translation | 9 | 7.14E-23 | 7.38E-21 |
| GO:0000398 | mRNA splicing, via spliceosome | 3 | 3.95E-21 | 3.62E-19 |
| GO:0071555 | cell wall organization | 3 | 3.95E-21 | 3.62E-19 |
| GO:0006349 | regulation of gene expression by genetic imprinting | 3 | 4.28E-21 | 3.54E-19 |
| GO:0010025 | wax biosynthetic process | 3 | 5.84E-21 | 4.39E-19 |
| GO:0009611 | response to wounding | 5 | 4.47E-19 | 3.08E-17 |
| GO:0006855 | drug transmembrane transport | 3 | 1.07E-17 | 6.77E-16 |
| GO:0009409 | response to cold | 6 | 7.87E-15 | 4.65E-13 |
| GO:0009553 | embryo sac development | 3 | 2.10E-12 | 1.15E-10 |
| GO:0048364 | root development | 4 | 2.84E-12 | 1.47E-10 |
| GO:0006629 | lipid metabolic process | 4 | 5.96E-11 | 2.90E-09 |
| GO:0009058 | biosynthetic process | 3 | 3.39E-09 | 1.56E-07 |
| GO:0009416 | response to light stimulus | 4 | 3.48E-08 | 1.51E-06 |
| GO:0016310 | Phosphorylation | 4 | 4.45E-08 | 1.84E-06 |
| GO:0009826 | unidimensional cell growth | 3 | 5.57E-08 | 2.19E-06 |
| GO:0009723 | response to ethylene | 3 | 7.02E-08 | 2.64E-06 |
| GO:0009751 | response to salicylic acid | 3 | 7.02E-08 | 2.64E-06 |
| GO:0006508 | Proteolysis | 6 | 1.36E-07 | 4.89E-06 |
| GO:0009555 | pollen development | 3 | 2.58E-07 | 8.86E-06 |
| GO:0006886 | intracellular protein transport | 3 | 3.09E-07 | 1.02E-05 |
| GO:0032259 | Methylation | 3 | 3.09E-07 | 1.02E-05 |
| GO:0055085 | transmembrane transport | 3 | 3.09E-07 | 1.02E-05 |
| GO:0045893 | positive regulation of transcription, DNA-templated | 3 | 4.61E-07 | 1.47E-05 |
| GO:0051301 | cell division | 3 | 7.84E-07 | 2.40E-05 |
| GO:0006511 | ubiquitin-dependent protein catabolic process | 3 | 7.84E-07 | 2.40E-05 |
| GO:0006952 | defense response | 6 | 9.34E-07 | 2.76E-05 |
| GO:0006457 | protein folding | 3 | 2.42E-06 | 6.90E-05 |
| GO:0006979 | response to oxidative stress | 3 | 2.42E-06 | 6.90E-05 |
| GO:0008152 | metabolic process | 3 | 3.55E-06 | 9.78E-05 |
| GO:0007275 | multicellular organism development | 3 | 4.73E-06 | 1.26E-04 |
| GO:0016567 | protein ubiquitination | 3 | 5.79E-06 | 1.49E-04 |
| UP-REGULATED | ||||
| GO:0006351 | transcription, DNA-templated | 14 | 7.89E-06 | 1.98E-04 |
| GO:0006355 | regulation of transcription, DNA-templated | 15 | 8.21E-06 | 1.99E-04 |
| GO:0055114 | oxidation-reduction process | 6 | 1.23E-05 | 2.90E-04 |
| GO:0006970 | response to osmotic stress | 5 | 3.37E-05 | 7.74E-04 |
| GO:0009737 | response to abscisic acid | 8 | 3.64E-05 | 8.11E-04 |
| GO:0009845 | seed germination | 4 | 3.82E-05 | 8.29E-04 |
| GO:0006396 | RNA processing | 4 | 3.84E-05 | 8.13E-04 |
| GO:0042542 | response to hydrogen peroxide | 3 | 5.36E-05 | 0.001106 |
| GO:0009636 | response to toxic substance | 3 | 5.78E-05 | 0.001163 |
| GO:0009408 | response to heat | 4 | 5.78E-05 | 0.001163 |
| GO:0009624 | response to nematode | 3 | 6.12E-05 | 0.001203 |
| GO:0009414 | response to water deprivation | 5 | 6.12E-05 | 0.001203 |
| GO:0009734 | auxin-activated signaling pathway | 4 | 6.53E-05 | 0.001253 |
| GO:0009738 | abscisic acid-activated signaling pathway | 4 | 7.53E-05 | 0.001412 |
| GO:0009908 | flower development | 4 | 1.07E-04 | 0.001968 |
| GO:0006470 | protein dephosphorylation | 3 | 1.29E-04 | 0.002319 |
| GO:0006810 | Transport | 5 | 1.29E-04 | 0.002319 |
| GO:0009651 | response to salt stress | 6 | 1.36E-04 | 0.00238 |
| GO:0015979 | Photosynthesis | 3 | 1.36E-04 | 0.00238 |
| GO:0009733 | response to auxin | 4 | 1.38E-04 | 0.002364 |
| GO:0007165 | signal transduction | 5 | 1.51E-04 | 0.00255 |
| GO:0009873 | ethylene-activated signaling pathway | 3 | 1.90E-04 | 0.003131 |
| GO:0009735 | response to cytokinin | 3 | 2.35E-04 | 0.003805 |
| GO:0035556 | intracellular signal transduction | 3 | 2.61E-04 | 0.004137 |
| GO:0042742 | defense response to bacterium | 3 | 2.61E-04 | 0.004137 |
| GO:0046686 | response to cadmium ion | 3 | 3.34E-04 | 0.005191 |
| GO:0005975 | carbohydrate metabolic process | 3 | 3.35E-04 | 0.005117 |
| GO:0009793 | embryo development ending in seed dormancy | 3 | 3.35E-04 | 0.005117 |