TABLE 3.

Selected overrepresented PANTHER molecular functions and biological processes in clusters 1 to 8b

ClusterOrganism and regulationaMolecular function(s)Biological processesPathway(s)
1 Streptococcus salivariusOther G protein modulator, transcription factor, actin-binding cytoskeletal protein, helicase, lyase, other chaperonesmRNA transcription, exocytosis, transport, phosphate metabolism, segment specification, neurotransmitter release, muscle contractionNicotinic acetylcholine receptor signaling
2 Streptococcus salivariusSerine/threonine protein kinase, cytoskeletal protein, double-stranded DNA binding proteinSignal transduction, cell structure and motility, cell adhesion, transport, cell proliferation and differentiation, phospholipid metabolism, developmental processes, natural killer cell-mediated immunityTGF-β signaling, FAS signaling, G protein signaling, presenilin, P53 by glucose deprivation, ATP synthesis
3 Salmonella serovar Typhimurium↑None at a P of <0.01Inhibition of apoptosis, developmental processes, cell structure and motility, nitrogen metabolism, cell proliferation and differentiationInflammation, apoptosis signaling, Toll receptor signaling, Ras, integrin signaling, insulin/IGF-MAPKK/MAPK, angiotensin II-stimulated signaling, EGF receptor signaling
4 Salmonella serovar Typhimurium↓Cadherin receptor G protein modulatorCell adhesion, developmental processes, G protein-mediated signaling, neurogenesis vasoconstriction/dilationCadherin signaling, G protein signaling, Wnt signaling, axon guidance mediated by semaphorins, inflammation, Parkinson's disease, histamine H1 receptor-mediated signaling, methylcitrate cycle
5 Staphylococcus aureusNone at a P of <0.01mRNA transcriptional regulationRas, oxidative-stress response, EGF receptor signaling, apoptosis signaling, B-cell activation, T-cell activation
6 Staphylococcus aureusImmunoglobulin receptor family, defense/immunity protein, serine protease inhibitor, extracellular matrix, apolipoproteinCell surface receptor-mediated signal transduction, neuronal activitiesBlood coagulation, lipoate biosynthesis
7 Pseudomonas aeruginosaReceptor, chemokine, cytokine, basic helix-loop-helix transcription factor, interleukinJNK cascade, macrophage-mediated immunity, NF-κB cascade, apoptosis, cell proliferation and differentiation, cytokine- and chemokine-mediated signaling pathway, calcium-mediated signaling, granulocyte-mediated immunity, T-cell-mediated protein phosphorylation, MAPKKK cascade, homeostasisApoptosis signaling, interleukin signaling, oxidative-stress response, blood coagulation, Wnt signaling, angiogenesis, presenilin, PDGF signaling, VEGF signaling
8 Pseudomonas aeruginosaExtracellular matrix, cadherin, guanyl-nucleotide exchange factor, voltage-gated potassium channel, acetylcholine receptor, ion channelSignal transduction, cell adhesion, developmental processes, transport, neuronal activitiesCadherin signaling, Wnt signaling, nicotinic acetylcholine receptor signaling, muscarinic acetylcholine receptor 2 and 4 signaling, endogenous cannabinoid signaling, 5-hydroxytryptamine biosynthesis, metabotropic glutamate receptor group ii, presenilin, G protein signaling
  • a ↑ signifies that genes in this cluster were upregulated;↓ signifies that genes in this cluster were downregulated.

  • b EGF, epidermal growth factor; IGF, insulin-like growth factor; JNK, Jun N-terminal kinase; MAPKKK, MAPK kinase kinase; TGF, transforming growth factor; VEGF, vascular endothelial growth factor.