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. 2006 Oct;74(10):5893–5902. doi: 10.1128/IAI.00489-06

TABLE 2.

Biological processes significantly altered in response to infection with PAO1 and the rsmA mutant

Gene Ontology annotation categorya EASE scoreb
Targets chosen for reverse transcription-PCR
Uninfected vs PAO1-infected cells Uninfected vs rsmA mutant-infected cells
Development 0.00327259 0.044995631 FGF18, KLF6c
Cell growth 0.003632335 NS
Regulation of transcription 0.004455422 NS Jun, FGF18, KLF2, KLF6
Immune cell activation 0.004748091 NS KLF6
Cell activation 0.004748091 NS KLF6
Regulation of transcription, DNA dependent 0.005062711 NS Jun, FGF18, KLF2, KLF6
Lymphocyte activation 0.010608842 NS KLF6
Transcription, DNA dependent 0.012742898 NS Jun, FGF18, KLF2, KLF6
Response to biotic stimulus 0.0163397 NS KLF6
Transcription 0.016418748 NS Jun, FGF18, KLF2, KLF6
Immune response 0.017303871 NS KLF6
Response to external stimulus 0.018355915 NS KLF6
Regulation of cellular process 0.019197391 NS FGF18
Regulation of biological process 0.021607717 NS FGF18
Regulation of neurotransmitter levels 0.022346738 0.009804003
Organogenesis 0.031143844 NS FGF18, KLF6
Regulation of cell growth 0.031228117 NS
Signal transduction 0.043411124 NS FGF18
Positive regulation of cell proliferation 0.046373762 NS FGF18
Morphogenesis 0.047113929 NS FGF18, KLF6
Phenol metabolism 0.048148555 NS
Defense response 0.049987952 NS KLF6
Cell communication NS 0.004495031
Lipid metabolism NS 0.020087184
Cell adhesion NS 0.021125648
Lipid catabolism NS 0.029643693
Amino acid derivative metabolism NS 0.037618284
Aromatic amino acid family metabolism NS 0.043814181
Cellular process NS 0.044110669
a

Gene Ontology categories for biological processes (http://www.geneontology.org) determined by EASE to be significantly overrepresented after infection with PAO1 or the rsmA mutant.

b

The EASE score measures the statistical significance of changes in the regulation of biological processes by comparing the number of genes that were seen to change experimentally to the total number of genes spotted on the U133A array that are annotated for that biological process. NS, not significantly altered (EASE score of >0.05 for uninfected versus infected cells).

c

While the biological process “development” was significantly overrepresented in response to infection with both PAO1 and the rsmA mutant, FGF18 and KLF6, which belong to this functional category, were significantly altered in response to infection with PAO1 only, not with the rsmA mutant.