Table 6.
Biological processes common in the EGF- and Retinoic acid-regulated genes
|
a |
||||
|
Gene ontology: Biological process |
EGF1&4hUP |
RA 1hDN |
||
| regulation of cell motion |
1.45E-07 |
5.00E-06 |
||
| regulation of cell proliferation |
1.65E-07 |
3.06E-04 |
||
| biological_process |
5.84E-07 |
1.68E-03 |
||
| regulation of cell migration |
6.33E-05 |
1.69E-05 |
||
| positive regulation of cell motility |
6.15E-04 |
1.43E-02 |
||
| negative regulation of programed cell death |
6.27E-04 |
4.43E-02 |
||
| positive regulation of cell migration |
4.30E-03 |
7.98E-03 |
||
| anatomical structure development |
5.71E-02 |
5.33E-03 |
||
| regulation of catalytic activity |
7.77E-02 |
3.55E-02 |
||
|
b |
||||
|
Gene ontology: Biological process |
EGF1&4hUP |
RA4hUP |
||
| regulation of signal transduction |
1.41E-07 |
4.46E-04 |
||
| biological_process |
5.84E-07 |
7.73E-05 |
||
| regulation of gene expression |
2.27E-05 |
1.05E-04 |
||
| signal transduction |
3.62E-05 |
3.42E-04 |
||
| cell communication |
4.12E-05 |
2.77E-03 |
||
| response to stress |
6.39E-05 |
8.06E-04 |
||
| regulation of transcription |
7.87E-05 |
2.86E-04 |
||
| negative regulation of programed cell death |
6.27E-04 |
4.51E-04 |
||
| regulation of apoptosis |
8.12E-04 |
4.33E-02 |
||
| response to external stimulus |
2.35E-03 |
4.24E-02 |
||
| negative regulation of apoptosis |
3.07E-03 |
3.61E-04 |
||
| positive regulation of signal transduction |
3.47E-03 |
4.51E-04 |
||
| positive regulation of metabolism |
4.70E-03 |
1.99E-02 |
||
| regulation of RNA metabolic process |
8.79E-03 |
4.78E-03 |
||
| phosphate metabolic process |
1.08E-02 |
8.40E-05 |
||
| regulation of transcription |
1.33E-02 |
6.50E-03 |
|
|
| regulation of transcription |
1.59E-02 |
5.92E-03 |
||
| 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 |
||
| |
EGF1&4hUP |
RA24hUP |
||
| biological_process |
5.84E-07 |
1.20E-08 |
||
| regulation of gene expression |
2.27E-05 |
1.57E-02 |
||
| signal transduction |
3.62E-05 |
5.27E-04 |
||
| cell communication |
4.12E-05 |
1.41E-03 |
||
| response to stress |
6.39E-05 |
3.79E-04 |
||
| regulation of transcription |
7.87E-05 |
6.83E-02 |
||
| negative regulation of programed cell death |
6.27E-04 |
3.76E-04 |
||
| regulation of apoptosis |
8.12E-04 |
1.03E-04 |
||
| response to wounding |
8.17E-04 |
5.89E-04 |
||
| response to external stimulus |
2.35E-03 |
4.81E-03 |
||
| regulation of cell adhesion |
3.01E-03 |
3.76E-02 |
||
| negative regulation of apoptosis |
3.07E-03 |
2.99E-04 |
||
| positive regulation of signal transduction |
3.47E-03 |
3.66E-02 |
||
| cell motion |
3.70E-03 |
7.55E-05 |
||
| positive regulation of metabolism |
4.70E-03 |
7.30E-03 |
||
| phosphate metabolic process |
1.08E-02 |
5.42E-02 |
||
| protein metabolic process |
5.42E-02 |
6.91E-03 |
||
| |
EGF24&48hUP |
RA24hUP |
||
| cell differentiation |
5.90E-05 |
1.23E-02 |
||
| biological_process |
1.32E-02 |
1.20E-08 |
||
| metabolic process |
3.16E-02 |
1.43E-03 |
||
|
c |
||||
|
Kinase |
EGF1&4hUP |
RA1hDN |
||
| MAPK1 |
2.51E-07 |
3.69E-03 |
||
| MAPK14 |
1.36E-05 |
3.33E-03 |
||
| MAPK3 |
1.70E-04 |
9.04E-05 |
||
| |
EGF1&4hUP |
RA4hUP |
||
| MAPK1 |
2.51E-07 |
3.31E-05 |
||
| MAPK14 |
1.36E-05 |
1.45E-03 |
||
| EGFR |
1.39E-05 |
6.66E-05 |
||
| MAPK3 |
1.70E-04 |
2.29E-05 |
||
| |
EGF1&4hUP |
RA24hUP |
||
| EGFR |
1.39E-05 |
2.17E-06 |
||
| INSR |
1.02E-04 |
2.86E-05 |
||
| ERBB2 |
5.35E-02 |
8.18E-03 |
||
| FYN |
5.36E-02 |
2.91E-02 |
||
|
d |
||||
|
T. F. |
EGF1&4hUP |
RA4hUP |
RA24hUP |
|
| RELA |
2.28E-03 |
3.99E-02 |
3.34E-02 |
|
| REL | 4.41E-03 | 4.19E-05 | 9.16E-02 | |
The early EGF-induced genes have extensive overlaps with both induced and suppressed genes by RA. a) Common processes in the EGF-induced and RA-suppressed genes 1 h after RA treatment. b) Common processes in the EGF-induced and RA-induced genes 4 h after RA treatment. c) Common kinase targets in the products of EGF-induced and RA-regulated genes. d) Only the NFkB family transcription factors have binding site overrepresented in both the EGF-induced and RA-regulated genes.