Table 3.
Biological processes common in the EGF-, Interferon-γ- and IL-1-regulated genes
|
a |
||
|
Gene ontology: Biological process |
EGF1&4hUP |
IFN4hUP |
| biological_process |
5.84E-07 |
6.38E-06 |
| signal transduction |
3.62E-05 |
1.59E-04 |
| response to stress |
6.39E-05 |
1.37E-04 |
| regulation of gene expression |
2.27E-05 |
1.82E-03 |
| regulation of apoptosis |
8.12E-04 |
1.07E-03 |
| cell communication |
4.12E-05 |
5.65E-03 |
| regulation of RNA metabolic process |
8.79E-03 |
4.84E-03 |
| regulation of transcription |
7.87E-05 |
1.50E-02 |
| regulation of transcription, |
1.33E-02 |
9.08E-03 |
| protein metabolic process |
5.42E-02 |
2.34E-05 |
| response to wounding |
8.17E-04 |
6.57E-02 |
| |
EGF24&48hUP |
IFN48hUP |
| biological_process |
1.32E-02 |
3.32E-16 |
| metabolic process |
3.16E-02 |
8.99E-14 |
|
Gene ontology: Biological process |
EGF1&4hDN |
IFN4hDN |
| response to external stimulus |
5.47E-04 |
1.79E-09 |
| tissue development |
6.50E-04 |
3.64E-05 |
| cell differentiation |
6.90E-04 |
5.94E-10 |
| keratinocyte differentiation |
1.42E-02 |
5.37E-04 |
| epidermis development |
8.64E-06 |
1.49E-02 |
| response to chemical stimulus |
2.22E-02 |
4.54E-08 |
| defense response |
2.05E-02 |
2.31E-03 |
| response to stress |
2.32E-02 |
2.67E-08 |
| |
EGF24&48hDN |
IFN48hDN |
| response to stress |
1.95E-06 |
9.50E-10 |
| response to external stimulus |
5.54E-04 |
4.70E-03 |
| regulation of cell proliferation |
2.87E-03 |
3.97E-03 |
| biological_process |
1.45E-02 |
3.66E-24 |
| regulation of cell cycle |
7.16E-02 |
1.01E-04 |
| tissue development |
7.13E-02 |
4.06E-02 |
|
b |
||
|
Gene ontology: Biological process |
EGF1&4hUP |
IL1&1hUP |
| regulation of cell proliferation |
1.65E-07 |
4.09E-08 |
| biological_process |
5.84E-07 |
3.75E-12 |
| regulation of signal transduction |
1.41E-07 |
2.34E-06 |
| regulation of gene expression |
2.27E-05 |
2.84E-12 |
| signal transduction |
3.62E-05 |
1.16E-06 |
| cell communication |
4.12E-05 |
4.90E-06 |
| response to stress |
6.39E-05 |
7.05E-11 |
| regulation of transcription |
7.87E-05 |
1.60E-12 |
| regulation of cell motion |
1.45E-07 |
9.43E-05 |
| negative regulation of cell proliferation |
5.55E-05 |
6.13E-05 |
| negative regulation of prog. cell death |
6.27E-04 |
5.05E-05 |
| regulation of apoptosis |
8.12E-04 |
3.33E-09 |
| response to wounding |
8.17E-04 |
7.63E-05 |
| regulation of cell migration |
6.33E-05 |
9.95E-04 |
| positive regulation of chemotaxis |
2.38E-04 |
1.68E-03 |
| negative regulation of apoptos |
3.07E-03 |
1.73E-04 |
| positive regulation of signal |
3.47E-03 |
1.15E-05 |
| positive regulation of metabolism |
4.70E-03 |
3.42E-08 |
| positive regulation of cell process |
1.64E-03 |
3.11E-03 |
| regulation of RNA metabolic process |
8.79E-03 |
1.06E-10 |
| phosphate metabolic process |
1.08E-02 |
1.26E-05 |
| regulation of transcription, |
1.33E-02 |
6.42E-11 |
| response to external stimulus |
2.35E-03 |
1.33E-02 |
| regulation of transcription |
1.59E-02 |
6.90E-10 |
| transmembrane receptor protein |
1.49E-02 |
1.59E-03 |
| positive regulation of gene expression |
3.33E-02 |
4.02E-06 |
| positive regulation of cell motility |
6.15E-04 |
3.31E-02 |
| protein metabolic process |
5.42E-02 |
1.31E-06 |
| regulation of catalytic activity |
7.77E-02 |
1.89E-08 |
| transforming growth factor beta pathway |
8.47E-02 |
6.35E-03 |
| positive regulation of transcription |
9.37E-02 |
1.88E-06 |
|
Gene ontology: Biological process |
EGF24&48hUP |
IL1&48hUP |
| biological_process |
1.32E-02 |
8.89E-19 |
| metabolic process |
3.16E-02 |
1.32E-16 |
| |
EGF1&4hDN |
IL1 1hDN |
| cell differentiation |
6.90E-04 |
3.12E-03 |
| epidermis development |
8.64E-06 |
1.60E-02 |
| keratinocyte differentiation |
1.42E-02 |
3.78E-03 |
| |
EGF24&48hDN |
IL1 48hDN |
| epidermis development |
5.18E-03 |
6.21E-03 |
| biological_process |
1.45E-02 |
1.75E-14 |
| response to stress |
1.95E-06 |
3.26E-02 |
| response to external stimulus |
5.54E-04 |
4.08E-02 |
| |
EGF1_4hUP |
EFNAs_DN |
| response to stress |
6.39E-05 |
3.67E-02 |
| |
EGF24_48hUP |
EFNAs_DN |
| biological_process |
1.32E-02 |
6.92E-03 |
| metabolic process |
3.16E-02 |
3.29E-02 |
| |
EGF1_4hUP |
RA4hDN |
| regulation of gene expression |
2.27E-05 |
8.66E-05 |
| regulation of transcription |
7.87E-05 |
2.69E-04 |
| cell communication |
4.12E-05 |
2.62E-03 |
| biological_process |
5.84E-07 |
5.66E-03 |
| signal transduction |
3.62E-05 |
6.86E-03 |
| regulation of RNA metabolic process |
8.79E-03 |
8.62E-05 |
| regulation of cell migration |
6.33E-05 |
1.03E-02 |
| regulation of apoptosis |
8.12E-04 |
1.01E-02 |
| regulation of transcription |
1.33E-02 |
1.88E-04 |
| regulation of transcription |
1.59E-02 |
6.81E-04 |
| regulation of cell motion |
1.45E-07 |
2.60E-02 |
| regulation of cell proliferation |
1.65E-07 |
4.18E-02 |
| positive regulation of metabolism |
4.70E-03 |
4.57E-02 |
| regulation of signal transduction |
1.41E-07 |
5.12E-02 |
| |
EGF1_4hDN |
EFNAs_UP |
| epidermis development |
8.64E-06 |
9.39E-09 |
| tissue development |
6.50E-04 |
1.52E-05 |
| cell differentiation |
6.90E-04 |
1.80E-07 |
| keratinocyte differentiation |
1.42E-02 |
1.58E-11 |
| |
EGF24_48hDN |
EFNAs_UP |
| epidermis development |
5.18E-03 |
9.39E-09 |
| biological_process |
1.45E-02 |
5.83E-04 |
| tissue development |
7.13E-02 |
1.52E-05 |
| |
EGF1_4hUP |
RA4hUP |
| biological_process |
5.84E-07 |
7.73E-05 |
| regulation of gene expression |
2.27E-05 |
1.05E-04 |
| regulation of transcription |
7.87E-05 |
2.86E-04 |
| signal transduction |
3.62E-05 |
3.42E-04 |
| regulation of signal transduction |
1.41E-07 |
4.46E-04 |
| response to stress |
6.39E-05 |
8.06E-04 |
| negative regulation of program |
6.27E-04 |
4.51E-04 |
| cell communication |
4.12E-05 |
2.77E-03 |
| negative regulation of apoptosis |
3.07E-03 |
3.61E-04 |
| positive regulation of signal |
3.47E-03 |
4.51E-04 |
| phosphate metabolic process |
1.08E-02 |
8.40E-05 |
| regulation of RNA metabolic process |
8.79E-03 |
4.78E-03 |
| regulation of transcription, |
1.33E-02 |
6.50E-03 |
| regulation of transcription |
1.59E-02 |
5.92E-03 |
| positive regulation of metabolism |
4.70E-03 |
1.99E-02 |
| regulation of apoptosis |
8.12E-04 |
4.33E-02 |
| response to external stimulus |
2.35E-03 |
4.24E-02 |
| positive regulation of gene expression |
3.33E-02 |
1.35E-02 |
| protein metabolic process |
5.42E-02 |
1.39E-03 |
| positive regulation of transcription | 9.37E-02 | 7.29E-03 |
a) The EGF and Interferon-γ overlaps b) The EGF and IL-1 overlaps. UP denotes induced, DN suppressed genes. The numbers represent the p-values. While many ontological categories are redundant, closely related or overly general, note that keratinocyte differentiation is suppressed in all three sets, the EGF-, Interferon-γ-, and IL-1-regulated genes. Also note that processes related to cell motility are induced by EGF and IL-1, but not by IFNγ.