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. Author manuscript; available in PMC: 2013 Dec 1.

Published in final edited form as: Nat Biotechnol. 2013 Apr 21;31(6):522–529. doi: 10.1038/nbt.2530

Expression of individual metabolic pathways in tumors. The biochemical pathways defined in the KEGG database (see Supplementary Table 5 for pathway numbering) are shown in the coordinates of ( $\bar{n} + \bar{m}$ , horizontal axis) and ( $\bar{n} - \bar{m}$ , vertical axis), where $\bar{n}$ is the average fraction of tumor samples in which a pathway is significantly up-regulated, and $\bar{m}$ is the average fraction in which a pathway is significantly down-regulated. The averages $\bar{n}$ and $\bar{m}$ were calculated across all 22 tumors. The up- (down-) regulation significance was determined using Wilcoxon signed-rank test (FDR-corrected P-value < 0.05, see Supplementary Fig. 4b for the same analysis with FDR = 0.2). Several pathways are highlighted using different colors. The dashed lines demarcate the region where $\bar{n} - \bar{m}$ is less than 20% of $\bar{n} + \bar{m}$ and are shown for visualization purposes only. Metabolic pathways without significant expression changes are primarily clustered on the left of the figure. Pathways that are often significantly up-regulated (high $\bar{n}$ values) occupy positions in the upper right corner, while pathways that are primarily down-regulated (high $\bar{m}$ values) occupy positions in the lower right corner. Highly heterogeneous pathways that show, in different tumors, both significant up- and down-regulation are clustered on the right near zero on the vertical axis.