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-

genes 1 h after RA treatment. b) Common processes in the EGF-induced and RA- 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.

Blumenberg

Blumenberg BMC Genomics 2013 14:85   doi:10.1186/1471-2164-14-85

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