Canonical pathways involving deregulated genes.
Panel A shows the top 25 canonical pathways identified in the set of 2,006 deregulated genes in the whole set of tumors. Panel B shows the top 25 canonical pathways identified in the set of 862 genes deregulated exclusively in high-CN tumors. The canonical pathways were identified with the Ingenuity Pathway Analysis software. The -log (p value) and ratio were calculated by comparing the number of genes belonging to the pathway present in the data sets with the human genome database. The p value was calculated using the chi-square or Fisher’s exact test, as appropriate, and values of -log (p value) higher than 1.3 (red line) correspond to a value of p<0.05. The canonical pathway of hypoxia inducible factor (HIF1α) signaling was statistically significant in the deregulated genes in the whole set (43rd place) and in the high-CN set of tumors (26th place).