Background and aim To study changes of proteins after zinc finger protein 139 (ZNF139) gene was inhibited in gastric cancer cell line BGC823, and to explore regulation mechanisms of ZNF139 to gastric cancer cells.Methods siRNA-specific ZNF139 was synthesized and transfected into gastric cancer cell line BGC823; 2-D fluorescence difference gel electrophoresis (2-D DIGE) and liquid chromatography-mass spectrometry (LC-MS) were applied to screen, identify differentially expressed proteins in BGC823 cells before and after transfection, and function of these proteins was analyzed; Western blot method was applied to verify the identified proteins.Results ZNF 139 expression in siRNA transfected cancer cell BGC823 was significantly decreased; before and after transfection 2-D DIGE was used to analyze and identify eight distinct differential protein spots were analyzed and identified in transfected and non-transfected BGC823 cells with 2-D DIGE, of which seven were identified with LC-MS technology, including switches associated protein 70, far upstream element binding protein 1, heat shock protein 60, annexin A7, small ubiquitin-like modifier 1 activating enzyme (SUMOl-activating enzyme), chaperonin-containing tail-less complex protein 1 and annexin A2.Bioinformatic analysis was applied, and these proteins were found to be associated with proliferation, apoptosis, invasion, metastasis and adhesion of gastric cancer cells.Western blot analysis confirmed that expressions of these proteins in BGC823 were consistent with those in the proteomic results.Conclusion ZNF139 gene may influence the biological behavior of gastric cancer cells in many ways by regulating multiple genes and protein expressions.