Table 2.
U133 (REF) (Number of genes) | SDK down (Number of genes) | Expected (Number of genes) | P-value | |
---|---|---|---|---|
Biological process | ||||
mRNA transcription | 1462 | 92 | 32.21 | 2.33E−20 |
mRNA transcription regulation | 1205 | 80 | 26.55 | 6.16E−19 |
Nucleoside, nucleotide and nucleic acid metabolism | 2607 | 122 | 57.44 | 6.12E−17 |
Developmental processes | 1776 | 62 | 39.13 | 1.94E−04 |
Cell cycle control | 354 | 19 | 7.8 | 4.08E−04 |
MAPKKK cascade | 194 | 13 | 4.27 | 4.58E−04 |
Stress response | 164 | 11 | 3.61 | 1.22E−03 |
Other developmental process | 94 | 8 | 2.07 | 1.31E−03 |
Angiogenesis | 31 | 4 | 0.68 | 5.23E−03 |
Cell proliferation and differentiation | 621 | 24 | 13.68 | 6.20E−03 |
Oncogenesis | 499 | 20 | 10.99 | 8.25E−03 |
Molecular function | ||||
Transcription factor | 1602 | 102 | 35.3 | 4.04E−23 |
Nucleic acid binding | 2121 | 90 | 46.73 | 5.85E−10 |
Zinc finger transcription factor | 619 | 38 | 13.64 | 1.97E−08 |
Transcription cofactor | 137 | 16 | 3.02 | 1.08E−07 |
Other transcription factor | 341 | 24 | 7.51 | 9.02E−07 |
Nuclease | 220 | 14 | 4.85 | 4.66E−04 |
KRAB box transcription factor | 423 | 20 | 9.32 | 1.35E−03 |
Chromatin/chromatin-binding protein | 106 | 8 | 2.34 | 2.73E−03 |
Homeobox transcription factor | 166 | 10 | 3.66 | 4.26E−03 |
Other zinc finger transcription factor | 100 | 7 | 2.2 | 7.32E−03 |
Other signaling molecule | 154 | 9 | 3.39 | 7.88E−03 |
HMG box transcription factor | 36 | 4 | 0.79 | 8.73E−03 |
Pathway | ||||
Transcription regulation by bZIP transcription factor | 42 | 5 | 0.93 | 2.59E−03 |
Interferon-gamma signaling pathway | 32 | 4 | 0.71 | 5.83E−03 |
Wnt signaling pathway | 289 | 13 | 6.37 | 1.30E−02 |
TGF-beta signaling pathway | 105 | 6 | 2.31 | 3.02E−02 |
Hedgehog signaling pathway | 33 | 3 | 0.73 | 3.74E−02 |
Apoptosis signaling pathway | 123 | 6 | 2.71 | 5.69E−02 |
aPanther analysis was done on the 460 transcripts with ≥2.5-fold decrease in expression after SDK treatment. Only classes found to be over-represented among SDK down-regulated genes and with lowest P-values are shown.