Contingency tables for genes identified using two different filtering schemes. (a) A431, (b) U251MG and (c) U2OS cell lines. CN/TRX (+) denotes genes for which the average Spearman coefficient over all three cell lines for the relationship between copy number and transcription is >0.8. NEA (+) denotes genes exhibiting enriched connectivity to genes carrying damaging mutations in the same cell line (NEA z-score >1.96). These criteria were selected to optimize the 'sensitivity/specificity' trade-off after having considered several alternatives (Figure S4 in Additional file 1). In the network diagrams in the same cell line order, red triangles denote CNA genes coupled with more than five links to genes carrying damaging SNVs in the same line, denoted as green diamonds. The color scheme for the connections is: red lines for physical protein interaction, blue lines for mRNA co-expression, green lines for protein co-expression, purple lines for sub-cellular co-localization, khaki lines for coherence of Gene Ontology annotation, deep bluish green lines for links in a KEGG pathway, and deep blue lines for known members of the same complex.