0000000001303359
AUTHOR
Yuri Tolkach
Additional file 1: of Where is the limit of prostate cancer biomarker research? Systematic investigation of potential prognostic and diagnostic biomarkers
Supplementary Data. List of abbreviations. (PDF 29 kb)
Integrative clinical transcriptome analysis reveals TMPRSS2-ERG dependency of prognostic biomarkers in prostate adenocarcinoma.
In prostate adenocarcinoma (PCa), distinction between indolent and aggressive disease is challenging. Around 50% of PCa are characterized by TMPRSS2‐ERG (T2E)‐fusion oncoproteins defining two molecular subtypes (T2E‐positive/negative). However, current prognostic tests do not differ between both molecular subtypes, which might affect outcome prediction. To investigate gene‐signatures associated with metastasis in T2E‐positive and T2E‐negative PCa independently, we integrated tumor transcriptomes and clinicopathological data of two cohorts (total n = 783), and analyzed metastasis‐associated gene‐signatures regarding the T2E‐status. Here, we show that the prognostic value of biomarkers in PCa…
Where is the limit of prostate cancer biomarker research? Systematic investigation of potential prognostic and diagnostic biomarkers
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 f…
Additional file 7: of Where is the limit of prostate cancer biomarker research? Systematic investigation of potential prognostic and diagnostic biomarkers
Table S6 Top 50 genes with statistically significant and independent association with biochemical recurrence-free survival in multivariate Cox regression analysis (dichotomization using median) in patients with prostate cancer. Estimates of their perspectivity for further research are provided. (PDF 65 kb)
Additional file 6: of Where is the limit of prostate cancer biomarker research? Systematic investigation of potential prognostic and diagnostic biomarkers
Table S5 Full results of the multivariate Cox regression analysis for single genes. (TXT 1949 kb)
Additional file 3: of Where is the limit of prostate cancer biomarker research? Systematic investigation of potential prognostic and diagnostic biomarkers
Table S2 Full results of Gene Set Enrichment Analysis (GSEA) for tumor vs normal tissue using Gene Ontology Biological Processes database. (TXT 131 kb)
Additional file 2: of Where is the limit of prostate cancer biomarker research? Systematic investigation of potential prognostic and diagnostic biomarkers
Table S1 Pairwise comparison of the gene expression of normal and tumor tissue using negative binomial generalized log-linear model and correction for false discovery rate (FDR). (TXT 2100 kb)
Additional file 5: of Where is the limit of prostate cancer biomarker research? Systematic investigation of potential prognostic and diagnostic biomarkers
Table S4 Correlation between ISUP histological grade group of the tumor (dichotomized as high-grade, ≥4 + 4, vs low-grade tumors) and mRNA expression of single genes. Correlation analysis for ISUP grade groups (Groups 1–5) is provided in parallel for comparison. Delta of Pearson r correlation levels is calculated for these 2 different settings. (TXT 2104 kb)
Additional file 4: of Where is the limit of prostate cancer biomarker research? Systematic investigation of potential prognostic and diagnostic biomarkers
Table S3 Correlation between ISUP histological grade group of the tumor (Grade groups 1â 5) and mRNA expression of single genes, univariate Cox-regression analysis with biochemical recurrence as an endpoint. Full list of genes (nâ =â 17,681). (TXT 3078 kb)
Additional file 8: of Where is the limit of prostate cancer biomarker research? Systematic investigation of potential prognostic and diagnostic biomarkers
Table S7 Results of the multivariate Cox regression analysis for single genes separately for patients of ISUP grade groups 2â 5. (TXT 1940 kb)