PTEN and neoplasm: These factors capture sets of genes potentially exhibiting cis-effects, interesting examples include (1) Factor 94 which captures the co-amplification and overexpression of the MYC oncogene along with its proximal genes (ASAP1, PTK2; Supplementary Fig. 6); and (2) Factor 58 which captures the mutations and decreased expression levels of PTEN, RB1, and TP53 all of which are tumor suppressors (Supplementary Fig. 7).