Fig. 3

Mutually exclusive (ME) and co-occurring (CO) associations at the level of hallmarks. a Bar diagram depicting the total number of significant ME and CO associations found across all cancer types divided into three categories: pathway pairs, hallmark pairs, and control pairs. The grey bars in the background indicate the expected number of associations under the assumption that ME and CO associations are evenly distributed across the three categories. b Overview of ME and CO associations at the level of cancer hallmarks, i.e., associations found between pairs of genes that are not part of the same pathway but link to the same hallmark. The color indicates whether the majority of detected associations were ME (blue) or CO (red). The most significant ME association for each combination of a cancer type and a hallmark is printed in the bottom-right corner of the box, if available. Similarly, the most significant CO association is printed in the top-left corner of the box, if available. Genes with an asterisk are significantly frequently mutated in the respective cancer type as determined by the Mutational Significance in Cancer (MuSiC) or Genomic Identification of Significant Targets In Cancer (GISTIC), i.e., they are either frequently mutated or show recurrent copy number loss or gain. c Tail strengths (TSs) including the 95% confidence intervals (CIs) for the three categories: pathway pairs, hallmark pairs, and control pairs. Significant differences between TSs are indicated by a red asterisk. CALM1 calmodulin 1 (phosphorylase kinase, delta), GNA11 guanine nucleotide binding protein (G protein), alpha 11 (Gq class), EBI3 Epstein-Barr virus induced 3, APOB apolipoprotein B, FADD Fas (TNFRSF6)-associated via death domain, ATM ATM serine/threonine kinase, PRKDC protein kinase, DNA-activated, catalytic polypeptide, BRCA2 breast cancer 2, CD79B CD79b molecule, immunoglobulin-associated beta, PRKACA protein kinase, cAMP-dependent, catalytic, alpha, PDGFRA platelet-derived growth factor receptor, alpha polypeptide, CCND1 cyclin D1, FGFR1 fibroblast growth factor receptor 1, PLD1 phospholipase D1, phosphatidylcholine-specific, LRP2 low-density lipoprotein receptor-related protein 2, ARHGAP35 Rho GTPase activating protein 35, STRADA STE20-related kinase adaptor alpha, RB1 retinoblastoma 1, AGAP2 ArfGAP with GTPase domain, ankyrin repeat and PH domain 2, LMNB2 lamin B2, ATR ATR serine/threonine kinase, ANTXR1 anthrax toxin receptor 1, BAG4 BCL2-associated athanogene 4, SMAD4 SMAD family member 4; ERBB2, erb-b2 receptor tyrosine kinase 2, RELN reelin, DVL3 dishevel segment polarity protein 3, EFNA2 ephrin-A2. Other abbreviations as in Fig. 2