Aim. To analyze an expression pattern of the cancer-associated genes in prostate tumors at mRNA and protein levels and find putative association between the expression of these genes and the genes, controlling epithelial to mesenchymal cell transition (EMT), the markers of prostate cancer and stromal elements. Methods. Relative expression of genes was assessed by a quantitative PCR in 29 prostate cancer tissue samples (T) of different Gleason score (GS) and tumor stage, 29 paired conventionally normal prostate tissue (CNT) samples and in 14 samples of prostate adenomas (A). Immunohistochemistry (IHC) was used to assess protein expression. Results. We found significant differences (p<0.05) in RE of three genes (FOS, PLAU, EPDR1) between the T, N and A groups. FOS was induced in T and CNT, compared with A whereas PLAU and EPDR1 were decreased. Noteworthy, RE of the five genes (FOS, EFNA5, TAGLN, PLAU and EPDR1) changed significantly, depending on GS (p<0.05) in T, compared to the A and/or CNT groups. Moreover, according to the K-means clustering, RE of the FOS, PLAU and EDPR1 genes varied in the tumor groups, consisting of cancers with different GS. The FOS protein signal was higher in adenocarcinomas, compared to hyperplasia. The same trend was demonstrated by q-PCR. FOS expression increased upon the tumor development i.e. was higher in the tumors at stage 3-4. PLAU expression was decreasing meanwhile, as was shown by q-PCR and IHC. Conclusions. IHC data allowed us to understand the high levels of RE dispersion. Mainly, it is due to the expression in other cell types, and not in the prostate gland cells. For the meaningful clustering, prognosis and also for the creation of specific biomarker panels, these two methods should be adequately merged.