Table 2 Top 10 pathways with the most difference in expression between the three perturbation classes. The second column shows the specific experimental conditions in the perturbation classes that were most different. The Difference Score was calculated using the t-values of the pathway nodes in the given conditions

Regulation of Complement cascade

Diet.Add.Probio.BALBc.C - Drug.HerbalDrug.SPF.C - IC.STyph.4 day.SB1117.C

APC/C:Cdc20 mediated degradation of Cyclin B

Diet.Add.Heme.C - Drug.Antibiotics.C - IC.GDuodenalis.SI

Cdc20:Phospho-APC/C mediated degradation of Cyclin A

Diet.Add.Heme.C - Drug.Antibiotics.C - IC.Colitis.C

Inactivation of APC/C via direct inhibition of the APC/C complex

Diet.Add.Heme.C - Drug.Antibiotics.C - IC.Colitis.C

Formation of the HIV-1 Early Elongation Complex

Diet.Add.Probio.C57BL6.C - Drug.Antibiotics.C - IC.STyph.4 day.SL1344.C

Formation of HIV elongation complex in the absence of HIV Tat

Diet.Add.Probio.C57BL6.C - Drug.Antibiotics.C - IC.STyph.4 day.SL1344.C

Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal

Diet.Add.Heme.C - Drug.HerbalDrug.C - IC.Colitis.C

Signal regulatory protein (SIRP) family interactions

Diet.Fat.30.M.SI - Drug.Penicillin.SI - IC.STyph.4 day.SB1117.C

Termination of O-glycan biosynthesis

Diet.Add.Heme.C - Drug.HerbalDrug.C - IC.STyph.4 day.SB1117.C

Formation of HIV-1 elongation complex containing HIV-1 Tat

Diet.Add.Probio.C57BL6.C - Drug.Antibiotics.C - IC.STyph.4 day.SL1344.C