Fig. 1

Pathway analyses of the quantitative proteomics data. A. Statistical enrichment test in PANTHER using Biological Process and Molecular Function Gene Ontology annotations. Up- and down-regulated pathways are respectively indicated by red and blue bars. Significance limits for -log10 (p-value) (> 1.3, corresponding to p-value < 0.05) are indicated by dashed lines, and twelve pathways with the highest p-value from the statistical enrichment test are shown. B. Ingenuity Pathway Analysis (IPA) using Canonical Pathway, and Disease and Toxicity annotations. Activated and inactivated pathways are respectively indicated by red and blue bars. Significance limits for the z-score (< -2.0 or > 2.0) are indicated by dashed lines. IPA calculates the z-score for a pathway as z = (N₊ - N₋) / √N, where N₊ and N₋ are respectively the numbers of (detected) up- and downregulated protein in the pathway, and N is the total number of detected proteins in the pathway. For the Canonical Pathways, twelve pathways with the highest z-score are shown, whereas all significant pathways are shown for the Disease and Toxicity Functions. For all analyses, N is number of proteins in the given pathway that were quantified by mass spectrometry