Table 3 Selected GO biological process terms over- and underrepresented among genes called up and down.
From: Transcriptional profiles underlying parent-of-origin effects in seeds of Arabidopsis thaliana
sample | GO term | no. (%) in sample | no. (%) in all genes | P-value bold = underrepresented |
|---|---|---|---|---|
all genes in experiment n = 11,091 annotated | Â | Â | Â | Â |
2xX4x down n = 71 annotated | response to stimulus | 15(21.12) | 817(7.3) | 0.00159 |
| Â | regulation of transcription, DNA-dependent | 8(11.26) | 374(3.37) | 0.0181 |
2xX6x up n = 228 annotated | cell wall organization and biogenesis | 8 (3.5) | 80 (0.72) | 0.0371 |
| Â | inorganic anion transport | 4(1.75) | 20(0.18) | 0.0483 |
2xX6x down n = 302 annotated | microtubule-based movement | 9(2.98) | 26(0.23) | 2.56 e-06 |
| Â | regulation of cell cycle | 7(2.31) | 38(0.34) | 0.00426 |
| Â | steroid metabolic process | 4(1.32) | 18(0.16) | 0.0373 |
fis1X2x up n = 304 annotated | carbohydrate metabolic process | 27(8.88) | 351(3.16) | 7.88 e-06 |
fis1x2x down n = 541 annotated | biosynthetic process | 16(2.77) | 773(6.96) | 0.0342 |
| Â | electron transport | 33(6.09) | 352(3.17) | 0.0295 |
| Â | regulation of biological process | 63(11.64) | 838(7.55) | 0.0342 |
| Â | regulation of cell cycle | 8(1.47) | 38(0.34) | 0.0345 |
| Â | sequestering of lipid | 4(0.73) | 8(0.72) | 0.0342 |
| Â | response to chemical stimulus | 31(5.73) | 348(3.13) | 0.0399 |
4x X 2x up n = 219 annotated | cellular process | 44(20.09) | 3665(33.0) | 0.0141 |
6xX2x up n = 554 annotated | defense response | 30(5.41) | 189(1.70) | 8.11 e-09 |
| Â | response to stimulus | 67(12.09) | 817(7.36) | 0.00345 |
| Â | response to starvation | 5(0.9) | 14(0.13) | 0.019 |
| Â | macromolecule metabolic process | 73(13.17) | 2300(20.74) | 0.00246 |
6xX2x down n = 697 annotated | translation | 41(5.88) | 276(2.49) | 2,76 e-06 |
| Â | macromolecule biosynthetic process | 48(6.88) | 380(3.42) | 5.57 e-05 |
| Â | macromolecule metabolic process | 185(26.54) | 2300(20.73) | 0.00551 |
| Â | DNA replication initiation | 4(0.57) | 7(0.06) | 0.0207 |
| Â | transcription factor import into nucleus | 3(0.43) | 4(0.04) | 0.0367 |
| Â | DNA metabolic process | 29(4.16) | 168(1.5) | 2.76 e-06 |
| Â | nucleosome assembly | 11(1.57) | 28(0.25) | 5.57 e-05 |
| Â | chromatin assembly and disassembly | 12(1.72) | 38(0.34) | 0.00019 |
| Â | organelle organization and biogenesis | 42(6.02) | 291(2.62) | 2.76 e-06 |
| Â | cellular component organization and biogenesis | 63(9.03) | 618(5.57) | 0.00282 |
| Â | microtubule-based movement | 7(1.0) | 26(0.23) | 0.0358 |