Table 2. PathVisio results of significant pathways found in the dataset by Varambally et al. comparing processed data provided by ArrayExpress with the reprocessed data.

Pathway	Z Score (ArrayExpress)	Z Score (Standardized processing)
Cholesterol Biosynthesis	4.14	3.65
Glutathione metabolism	2.67	1.59
Striated Muscle Contraction	2.17	0.78
Endochondral Ossification	2.12	1.32
Delta-Notch Signaling Pathway	2.12	0.68
Hedgehog Signaling Pathway	2.10	2.53
Calcium Regulation in the Cardiac Cell	1.96	2.29
Eicosanoid Synthesis	1.53	1.94
Prostaglandin Synthesis and Regulation	1.34	2.51
Id Signaling Pathway	1.14	2.52
Selenium	0.98	2.84
Nicotine Activity on Dopaminergic Neurons	0.69	2.25
Cytoplasmic Ribosomal Proteins	0.10	2.48
Irinotecan Pathway	0.07	2.57
Ganglio Sphingolipid Metabolism	−0.21	2.47
Sulfation	−0.34	1.95

Pathway analysis is based on a comparison between benign prostate tissue and primary prostate cancer. Only significant pathways with a Z-score >1.9 in at least one of the two analyses are included. Significant Z-scores are depicted in bold; matches in pathways between the analyses are in italics.