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Background  The identification of appropriate biomarkers is essential to support important clinical decisions in patients with prostate cancer. The aim of our study was a systematic bioinformatical analysis of the mRNA expression of all genes available for the prostate adenocarcinoma cohort of The Cancer Genome Atlas (TCGA), regarding their potential prognostic and diagnostic role.    Methods  The study cohort comprises 499 patients (TCGA prostate cancer cohort). mRNA expression data were available for approx. 20,000 genes. The bioinformatical statistical pipeline addressed gene expression differences in tumor vs. benign prostate tissue (including gene set enrichment analysis, GSEA) in samples from tumors with different aggressivenesses (Gleason score), as well as prognostic values in multistep survival analyses.    Results  Among all genes analyzed, 1754 were significantly downregulated and 1553 genes were significantly upregulated in tumor tissue. In GSEA, 16 of 30 top enriched biological processes were alterations of epigenetic regulation at different levels. Significant correlation with Gleason Score was evident for 8724 genes (range of Pearson r-values 0.09–0.43; all  p  < 0.05). In univariate Cox regression analyses, mRNA expression of 3571 genes showed statistically significant association with biochemical recurrence-free survival with a range of hazard ratios 0.3–3.8 ( p -value 7.4e− 07 to 0.05). Among these, 571 genes were independently associated with biochemical recurrence in multivariate analysis. Access to the full database including results is provided as supplement.    Conclusions  In our systematic analysis we found a big number of genes of potential diagnostic and prognostic value, many of which have not been studied in prostate cancer to date. Due to the comprehensive nature of this analysis and free access to the results, this study represents a reference database for prostate cancer researchers which can be used as a powerful tool for validation purposes and planning of new studies.    Electronic supplementary material  The online version of this article (10.1186/s12894-019-0479-z) contains supplementary material, which is available to authorized users.

Where is the limit of prostate cancer biomarker research? Systematic investigation of potential prognostic and diagnostic biomarkers