Table 2.

Pathways with the largest location or expression changes

Tissue	L:P	E:P	L:A	E:A	Pathway
Breast	+	—	—	—	HTLV I infection
	+	—	—	—	One carbon pool by folate
	—	+	—	—	Proteasome
	—	+	—	—	ErbB signaling
Liver	+	—	—	—	Axon guidance
	—	+	—	—	GPI anchor biosynthesis
	—	+	—	—	Hypertrophic cardiomyopathy
	—	+	—	—	Dilated cardiomyopathy
Prostate	+	—	—	—	Fatty acid elongation
	+	—	—	—	HIF-1 signaling
	—	+	—	—	Oxidative phosphorylation
	—	+	—	—	PPAR signaling
	—	+	—	—	Viral myocarditis
Bladder	+	—	+	—	Hippo signaling
	—	+	—	—	NF-κB signaling
	—	+	—	—	p53 signaling
	—	+	—	—	Transcription misregulation in cancer
	—	+	—	—	Apoptosis
	—	+	—	—	Cell cycle
	—	+	—	—	mRNA surveillance
	—	+	—	—	Ribosome biogenesis

Pathway P values were calculated by using individual protein location (L) or expression (E) P values from the pipeline (L:P, E:P) and using P values from pathologist annotations (L:A, E:A). Plus symbol indicates pathway P < 0.01. Values for all pathways are in Dataset S3.