The identified gene sets included several pathways also enriched for copy number gains (Fig. 2g): IFNα and IFNγ signaling, MTORC1 signaling, response to UV light, and TNFa signaling via NF-kB. Increased expression of these gene sets was also identified in GSEA stratified by tumor type (Supplementary Fig. 8c, d and Supplementary Data 13). Here, TNF is linked to neoplasm.