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.

Blumenberg

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

Open Data