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

Pathway Name	Most different conditions	Difference Score
Regulation of Complement cascade	Diet.Add.Probio.BALBc.C - Drug.HerbalDrug.SPF.C - IC.STyph.4 day.SB1117.C	21.07
APC/C:Cdc20 mediated degradation of Cyclin B	Diet.Add.Heme.C - Drug.Antibiotics.C - IC.GDuodenalis.SI	20.07
Cdc20:Phospho-APC/C mediated degradation of Cyclin A	Diet.Add.Heme.C - Drug.Antibiotics.C - IC.Colitis.C	17.92
Inactivation of APC/C via direct inhibition of the APC/C complex	Diet.Add.Heme.C - Drug.Antibiotics.C - IC.Colitis.C	17.42
Formation of the HIV-1 Early Elongation Complex	Diet.Add.Probio.C57BL6.C - Drug.Antibiotics.C - IC.STyph.4 day.SL1344.C	16.96
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	16.09
Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal	Diet.Add.Heme.C - Drug.HerbalDrug.C - IC.Colitis.C	16.07
Signal regulatory protein (SIRP) family interactions	Diet.Fat.30.M.SI - Drug.Penicillin.SI - IC.STyph.4 day.SB1117.C	15.87
Termination of O-glycan biosynthesis	Diet.Add.Heme.C - Drug.HerbalDrug.C - IC.STyph.4 day.SB1117.C	14.73
Formation of HIV-1 elongation complex containing HIV-1 Tat	Diet.Add.Probio.C57BL6.C - Drug.Antibiotics.C - IC.STyph.4 day.SL1344.C	13.87