Table 7

Biological processes common in keratinocytes and other cell types
Gene ontology process Keratinocytes HeLa MCF10A HUVEC MCF7
EGF1&4hUP GSE6783_1hUP 4 h UP GSE6784_1hUP 4 h UP GSE10778_1hUP 6 h UP GSE13009_1hUP 4 h UP 48 h DN (!)
a* regulation of gene expression 2.27E-05 8.60E-07 5.40E-10 9.30E-07 7.98E-07 1.34E-07 1.42E-04 1.50E-12 2.22E-14 2.18E-04
regulation of transcription 7.87E-05 9.91E-08 2.90E-10 1.48E-06 3.52E-07 1.42E-09 4.16E-06 3.00E-11 1.71E-13 5.94E-05
regulation of RNA metabolic process 8.79E-03 1.64E-05 3.38E-08 1.44E-04 8.88E-05 1.83E-06 3.71E-04 1.47E-09 1.83E-11 3.06E-03
regulation of transcription 1.33E-02 1.15E-04 2.32E-08 1.43E-04 9.91E-05 3.02E-07 8.11E-05 8.37E-09 1.32E-10 1.23E-03
regulation of transcription 1.59E-02 2.54E-05 1.99E-09 7.78E-04 1.41E-02 4.72E-06 4.61E-06 4.42E-06 6.28E-05 2.24E-03
positive regulation of gene expression 3.33E-02 9.78E-01 4.61E-03 1.24E-04 6.09E-05 2.04E-04 1.67E-01 2.38E-02 2.64E-04 1.19E-01
positive regulation of transcription 9.37E-02 6.97E-01 2.09E-03 1.51E-04 5.38E-05 2.25E-04 8.84E-02 2.47E-02 1.73E-04 7.71E-02
b regulation of signal transduction 1.41E-07 3.63E-03 1.89E-03 6.60E-05 2.12E-04 1 1 9.89E-07 1.93E-04 1
signal transduction 3.62E-05 7.57E-02 6.05E-07 7.21E-11 4.10E-08 1 1 3.49E-10 4.23E-17 1
positive regulation of signal trans. 3.47E-03 2.41E-01 3.57E-03 4.67E-03 6.83E-02 1 1 1.39E-01 6.02E-01 1
response to external stimulus 2.35E-03 4.06E-01 1 8.03E-07 2.10E-01 1 1 1 1 1
negative regulation of signaling 9.10E-05 1 1 1 8.38E-01 1 1 1 1 1
c regulation of cell motion 1.45E-07 2.89E-02 4.73E-04 1.24E-02 5.93E-04 1 1 3.63E-04 6.91E-03 5.47E-01
regulation of cell migration 6.33E-05 1.23E-02 6.66E-03 5.19E-02 1.44E-03 1 1 2.50E-04 3.01E-03 1
positive regulation of cell motility 6.15E-04 2.41E-01 2.63E-02 6.38E-01 1 1 1 5.45E-03 7.82E-03 1
positive regulation of chemotaxis 2.38E-04 9.30E-02 2.13E-03 1 1 1 1 5.00E-01 4.97E-02 1
positive regulation of cell migration 4.30E-03 1.40E-01 9.60E-03 1 1 1 1 1.64E-03 1.73E-03 1
cell motion 3.70E-03 1.13E-01 7.39E-02 4.32E-01 2.75E-01 1 1 1 6.20E-01 1
d regulation of cell proliferation 1.65E-07 6.74E-03 1.76E-03 2.75E-03 6.40E-02 1 1 8.19E-04 1.59E-03 1
positive regulation of cell proliferation 1.64E-03 4.97E-02 9.70E-04 8.01E-03 1.51E-01 1 1 8.50E-03 4.71E-01 1
e negative regulation of prog. cell death 6.27E-04 1.86E-02 1.25E-03 1.58E-04 2.33E-04 1 4.82E-01 5.84E-02 2.87E-03 1
regulation of apoptosis 8.12E-04 6.24E-02 8.43E-05 3.80E-07 2.73E-06 1 8.22E-02 4.64E-03 4.10E-05 1
negative regulation of apoptos 3.07E-03 6.10E-02 2.80E-03 1.22E-04 4.83E-04 1 4.05E-01 4.69E-02 2.05E-03 1
positive regulation of metabolism 4.70E-03 4.24E-02 5.71E-04 2.01E-05 6.52E-09 1.68E-03 1 4.33E-04 4.40E-07 3.26E-03
regulation of catalytic activity 7.77E-02 6.24E-01 2.05E-04 2.31E-03 1.41E-06 1 1.41E-03 1.36E-04 2.64E-05 1
cell communication 4.12E-05 7.24E-02 2.42E-06 3.87E-11 9.10E-07 1 1 2.48E-09 1.97E-15 1
phosphate metabolic process 1.08E-02 4.54E-02 4.48E-06 1.12E-02 2.46E-04 1 1 5.72E-06 2.70E-06 1
response to stress 6.39E-05 8.57E-02 5.22E-02 2.15E-07 7.26E-07 3.42E-02 1 1 1 1
anatomical structure development 5.71E-02 1 2.87E-01 2.01E-02 1 1 1 1 5.53E-02 1
transforming growth factor beta pathway 8.47E-02 1.19E-01 1 4.14E-01 1 4.44E-03 1 1 1 2.94E-01
positive regulation of leukocycytes 1.40E-02 1 5.51E-01 2.75E-01 1 1 1 9.41E-02 1 1
cell adhesion 8.83E-03 1 1 5.33E-04 1 1 1 1 1 1
transmembrane receptor protein 1.49E-02 4.44E-01 1 8.14E-02 1 6.97E-02 1 1 1 1
response to wounding 8.17E-04 1 1 2.40E-05 2.37E-01 1 1 1 1 1
regulation of cell adhesion 3.01E-03 1 1 7.25E-05 6.46E-02 1 1 1 1 1
negative regulation of DNA binding 9.91E-02 1 1 1 1 1 1 1 1 3.53E-01
biological process 5.84E-07 1.83E-04 3.12E-14 3.61E-13 9.62E-15 6.34E-09 1.21E-07 1.43E-15 1.38E-21 3.52E-02
protein metabolic process 5.42E-02 1 1.54E-06 4.66E-04 6.72E-06 1.27E-06 8.12E-02 2.46E-05 5.42E-08 6.91E-01
EGF 24&48 h UP 48 h DN (!)
biological process 1.32E-02 1.83E-04 3.12E-14 3.61E-13 9.62E-15 6.34E-09 1.21E-07 1.43E-15 1.38E-21 1.08E-06
metabolic process 3.16E-02 1 4.33E-12 4.76E-05 2.73E-13 5.14E-15 6.13E-12 2.61E-05 2.83E-11 1.41E-07

The rightmost column shows the antiparallel overlap, i.e., with the genes suppressed by EGF in MCF7 cells. * Letters a – e indicate the fully or largely redundant biological processes.

Blumenberg

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

Open Data