In this study, we used X-tile software to calculate the cut-point of each marker tested through IHC and qPCR to divide the patients into low expression and high expression groups. These cut-points were on the basis of survival data. Hence, we thought that the cut-points could reveal the differences between low and high expression more realistically. Additionally, we used monoclonal antibodies of all these markers in IHC to try our best to make the results more specific and solid. However, polyclonal antibodies were used in some studies [25, 17, 21, 29, 37, 41–44]. We thought that different types of antibodies might also be the reason of the variable high expression rates among our study and some previous ones. Moreover, we applied C-index to compare the accuracy of prognostic prediction and nomogram, a visualized method based on several valuable parameters to illustrate the prognosis of individual patients in this study. Through C-index and nomogram, we found that the prognostic prediction of nomogram based on Oct4 and EpCAM, age and TNM stage had significantly better accuracy than TNM alone, which indicated that the expressions of Oct4 and EpCAM were valuable in prognosis prediction of patient with GC. The results suggested that we should not only focus on TNM stage, but also pay attention to some specific characteristics of patients and tumors. However, we found that few previous studies had applied these kinds of methods in GC.