Fig. 2
From: Membrane protein-regulated networks across human cancers
Quantification of systematically integrated method (SIM) and MPP (an MP with binding partners) community-regulated pathways in 15 cancer types. a Receiver operator characteristic curves of the prediction accuracy of our integrated scoring (SSIM) method (red), STRING (black), FpClass (blue), and generalized interologs (green). b Analysis of the significance of community-regulated pathways shared by at least three (left) and seven (right) cancers across six enrichment P value thresholds. Among 65 cancer-related pathways, MPP communities were significantly more likely to be involved in a specific pathway in distinct tumor types than was expected by 1000 random trials (P < 4 × 10−10, Wilcoxon signed-rank test). The box represents the interquartile range (IQR) and the horizontal line in the box is the median. The whiskers denote the lowest and highest values within 1.5 times IQR from the first and third quartiles, respectively. The black dots represent outliers. c Significance analysis of communities in 197 MP families (blue) for certain pathways shared by multiple cancers (≥3 or 7 types) across different thresholds of enrichment P values (for details, see Supplementary Figs. 14b and 15). d Meta-z-scores between The Cancer Genome Atlas RNA-seq data (n = 5922 tumors) and 15 independent microarray sets (n = 528 tumors) showing a high correlation (R = 0.78, P < 2.2 × 10−16, Pearson test). Meta-z-scores depict the statistical significance of associations between MPP communities and certain pathways across 15 cancers. Source data are provided as a Source Data file
