Background: Comparison of gene expression algorithms may be beneficial for obtaining disease pattern or grouping patients based on the gene expression profile. The current study aimed to investigate whether the knowledge within these data is able to group the ovarian cancer patients with similar disease pattern. Methods: Four different clustering methods were applied on 20 genes expression data of 37 women with ovarian cancer. All selected genes in this study had prominent roles in the control of the activity of the immune system, as well as the chemotaxis, angiogenesis, apoptosis, and etc. Comparison of different clustering methods such as K-means, Hierarchical, Density-Based Spatial Clustering of Applications with Noise (DBSCAN) and Expectation-Maximization (EM) algorithm was the other aim of the present study. In addition, the percentage of correct prediction, Robustness-Performance Trade-off (RPT), and Silhouette criteria were used to evaluate the performance of clustering methods. Results: Six out of 20 genes (IFN-γ, Foxp3, IL-4, BCL-2, Oct4 and survivin) selected by the Laplacian score showed key roles in the development of ovarian cancer and their prognostic values were clinically and statistically confirmed. The results indicated proper capability of the expression pattern of these genes in grouping the patients with similar prognosis, i.e. patients alive after 5 years or dead (62.12%). Conclusion: The results revealed the better performance for k-means and hierarchical clustering methods, and confirmed the fact that by using the expression profile of these genes, patients with similar behavior can be grouped in the same cluster with acceptable accuracy level. Certainly, the useful information from these data may contribute to the prediction of prognosis in ovarian cancer patients along with other features of patients.