MEMo automatically identifies mutually exclusive alterations targeting frequently altered genes that are likely to belong to the same pathway.
A built-in Gitools option sorts genes and samples within a heatmap to present the pattern of mutually exclusive alterations, which is one approach to visual exploration of driver genes that are involved in the same pathway [ 48].
For example, the mutually exclusive alteration of genes in a pathway is a characteristic of cancer drivers [ 5, 6, 47].
Conversely, mutually exclusive alterations observed in the two DIPG subgroups may influence the response to a given targeted agent.
Rodríguez-Celma, J. et al. Mutually exclusive alterations in secondary metabolism are critical for the uptake of insoluble iron compounds by Arabidopsis and Medicago truncatula.
Leiserson, M. D., Wu, H. T., Vandin, F. & Raphael, B. J. CoMEt: a statistical approach to identify combinations of mutually exclusive alterations in cancer.
However, these are not mutually exclusive alterations, appearing together in multiple tumors.
We identified multiple rare, but mutually exclusive, alterations targeting components of these complexes, as well as ANKRD11, an inhibitor of p160 co-activator complexes.
This suggests that scenarios exist, potentially induced by treatment, where co-activation of otherwise mutually exclusive alterations is selected for as potential resistance mechanisms.
Finally, an unbiased pathway analysis revealed multiple rare, but mutually exclusive, alterations linked to loss of activity of co-repressor complexes N-Cor and SMRT.
Given TERTp-mut is associated with both 1p19q codeletion and EGFR amplification, which are mutually exclusive alterations with opposite prognostic effects and TERTp-mut had a different effect in low- and high-grade gliomas, prompted us to refine our survival analysis.
