ERG fusion and PTEN loss are known to be co-enriched in unselected patients and functionally cooperate in oncogenesis, but we find that their statistical co-enrichment is only seen in human prostate cancer lacking FOXP1-SHQ1 deletion (P < 0.001, Fisher’s exact test, prostate TCGA cohort4). Here, FOXP1 is linked to prostate carcinoma.