The CMap similarly predicted the functional impact of the tumor suppressor KEAP1. Nineteen alleles of KEAP1 were subjected to L1000 profiling. Whereas over-expression of wild-type KEAP1 showed the expected CMap connection to knock-down of its transcriptional target NFE2L2, multiple alleles of KEAP1 lacked the NFE2L2 connection, suggesting that these were KEAP1 loss-of-function alleles. A subset of these alleles were recently functionally characterized and reported to result in loss of KEAP1 function, as predicted by the CMap analysis (Hast et al., 2014) (Figure S3C, left panel). A similar phenomenon was observed with alleles of the phosphatase PTEN, which negatively regulates PI3K activity. Whereas overexpression of wild-type PTEN showed connectivity to signatures of PI3K inhibitors, such connectivity was lost with PTEN mutations at residues M35 (mutated in Cowden's syndrome), G127 (important for active site conformation) and G129 (required for phosphatase activity) (Figure S3C, right panel).
