Figure 2. Analysis Pipeline.

(A) Boolean implications are extracted between copy number alteration and expression of a gene, DNA methylation and expression of a gene, and Boolean implications combining all three variables: if (gene is deleted or gene is methylated), then gene expression is low. (B) Boolean implications extracted between mutations and recurrent copy number alterations represented as broad Copy Number Alterations (CNAs) are used to build a hierarchy graph. (C) Boolean implications extracted between mutations and methylation are used to predict the role of a mutation in producing aberrant methylation.