Transcriptome-wide gene expression profiles of human DU145 prostate cancer cells were obtained for two different shRNA-knockdowns, one specific for the X-form of the gene USP9 (USP9X) and one combined knockdown of both the X- and Y-form of the gene (USP9X/Y, used to infer potential USP9Y-specific gene expression changes indirectly by comparing both knockdowns). Here, USP9Y is linked to prostate carcinoma.