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Background  Glioblastomas have a high degree of malignancy, high recurrence rate, high mortality rate, and low cure rate. Searching for new markers of glioblastomas is of great significance for improving the diagnosis, prognosis and treatment of glioma.    Methods  Using the GEO public database, we combined 34 glioma microarray datasets containing 1893 glioma samples and conducted genetic data mining through statistical analysis, bioclustering, and pathway analysis. The results were validated in TCGA, CGGA, and internal cohorts. We further selected a gene for subsequent experiments and conducted cell proliferation and cell cycle analyses to verify the biological function of this gene.    Results  Eight glioblastoma-specific differentially expressed genes were screened using GEO. In the TCGA and CGGA cohorts, patients with high  CBX3 ,  BARD1 ,  EGFR , or  IFRD1  expression had significantly shorter survival but patients with high  GUCY1A3  or  MOBP  expression had significantly longer survival than patients with lower expression of these genes. After reviewing the literature, we selected the  CBX3  gene for further experiments. We confirmed that  CBX3  was overexpressed in glioblastoma by immunohistochemical analysis of tissue microarrays and qPCR analysis of surgical specimens. The functional assay results showed that silencing  CBX3  arrests the cell cycle in the G2/M phase, thereby weakening the cell proliferation ability.    Conclusions  We used a multidisciplinary approach to analyze glioblastoma samples in 34 microarray datasets, revealing novel diagnostic and prognostic biomarkers in patients with glioblastoma and providing a new direction for screening tumor markers.    Electronic supplementary material  The online version of this article (10.1186/s12967-019-1930-3) contains supplementary material, which is available to authorized users.

Integrated analysis of 34 microarray datasets reveals CBX3 as a diagnostic and prognostic biomarker in glioblastoma