“…A total of 135 probe sets of this CodeSet target transcripts from 121 oncogenes, tumor suppressors, and gene fusion variants associated with prostate cancer and cancer in general. These genes were selected based on their association with cancer, specifically prostate cancer, according to the following criteria, supported by at least two publications: (1) have significant differential gene expression in prostate tumor versus normal comparison based on microarray gene expression profiling (data accessible at NCBI GEO database, accession GSE32448 [24]), including ERG [25, 26], ERG8 [27, 28], ANXA2 [29, 30], MYO6 [31, 32] and MAOA [32, 33]; (2) are regulated by androgen, such as AMACR [25, 34, 35], PSGR [36, 37], PCGEM1 [38, 39], [40, 41], and NKX3.1 [42, 43]; (3) are associated with prognosis of prostate cancer, such as AR [44, 45], EZH2 [46, 47], C-MYC [48, 49], PTEN [50, 51], and NCOA2 [52, 53]; (4) are associated with the ETS family of transcription factors detected in GSE32448 [54, 55]; (5) are commonly rearranged in prostate cancer [26, 56, 57]; (6) are involved in prostate cancer cell invasion, such as SPINK1 [58, 59], TFF3 [60, 61], MMP2 and MMP9 [62, 63]; (7) or are associated with multiple malignancies involving PDGF [64], RAS [65], VEGF [66], EGFR [67], TP53 [65, 68], Interleukin [52], and JAK/STAT signaling pathways [69, 70]. An additional 16 probe sets target five genes that distinguish prostate epithelial from stromal cells [71–74], and 11 house-keeping genes with minimal tumor-normal differential expression identified through gene expression profiling [24] were included as controls.…”