Table 4.

Pathway Analysis of Gene Expression Following Treatment With TCE (800 mg/kg or 6 mmol/kg) or PCE (1000 mg/kg or 6 mmol/kg) as Illustrated in Figure 5

Category	Term	Count	pValue	qValuea
Pathways significantly (q < 0.05) affected in liver by both TCE and PCE (Figure 5A)b
KEGG_PATHWAY	mmu03320:PPAR signaling pathway	11	3.0E-13	2.0E-11
UP_KEYWORDS	Oxidoreductase	11	1.6E-06	8.8E-05
GOTERM_CC_DIRECT	GO:0005789 ∼ endoplasmic reticulum membrane	9	3.9E-04	1.6E-02
Pathway significantly (q < 0.05) affected in liver only by TCE (Figure 5B)c
GOTERM_CC_DIRECT	GO:0005615 ∼ extracellular space	19	7.4E-05	8.5E-03
Pathways significantly (q < 0.05) affected in liver only by PCE (Figure 5C)d
GOTERM_CC_DIRECT	GO:0005739 ∼ mitochondrion	80	1.2E-08	2.3E-06
GOTERM_BP_DIRECT	GO:0006629 ∼ lipid metabolic process	33	1.7E-07	1.1E-04
GOTERM_CC_DIRECT	GO:0005789 ∼ endoplasmic reticulum membrane	33	4.8E-04	2.6E-02
GOTERM_CC_DIRECT	GO:0005777 ∼ peroxisome	15	3.1E-06	4.0E-04
KEGG_PATHWAY	mmu02010:ABC transporters	9	3.7E-05	4.3E-03
Pathways significantly (q < 0.05) affected in kidney by both TCE and PCE (Figure 5D)e
KEGG_PATHWAY	mmu03320:PPAR signaling pathway	7	4.8E-09	2.0E-07
KEGG_PATHWAY	mmu00071:Fatty acid degradation	4	1.0E-04	1.5E-03
Pathways significantly (q < 0.05) affected in kidney only by TCE (Figure 5E)
None
Pathways significantly (q < 0.05) affected in kidney only by PCE (Figure 5F)f
GOTERM_BP_DIRECT	GO:0055114 ∼ oxidation-reduction process	27	1.2E-06	7.5E-04
GOTERM_BP_DIRECT	GO:0006631 ∼ fatty acid metabolic process	13	1.2E-06	1.5E-03
KEGG_PATHWAY	mmu00982:Drug metabolism-cytochrome P450	10	1.5E-06	8.2E-05
GOTERM_CC_DIRECT	GO:0005777 ∼ peroxisome	10	6.4E-05	6.5E-03
GOTERM_CC_DIRECT	GO:0005743 ∼ mitochondrial inner membrane	16	2.2E-04	1.5E-02

Representative pathways for each annotation cluster are shown, complete lists of significant pathways and clusters are included in Supplementary Tables 13–17.

^aBenjamini-Hochberg-corrected P value.

^bFull list of the significant pathways is in Supplementary Table 13.

^cFull list of the significant pathways is in Supplementary Table 14.

^dFull list of the significant pathways is in Supplementary Table 15.

^eFull list of the significant pathways is in Supplementary Table 16.

^fFull list of the significant pathways is in Supplementary Table 17.