Background and aim:Znic finger protein 139 (ZNF139) gene is proved play an important role in gastric cancer. Aim of this study is to identify changes of proteins after ZNF139 gene was inhibited in gastric cancer cell line BGC823 Methods: siRNA-specific ZNF139 was synthesized and transfected into 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, and function of these proteins was analyzed; Western blot method was applied to verify the identified proteins. Results: ZNF139 expression in siRNA transfected cancer cell BGC823 decreased significantly. Results of 2-D DIGE showed eight differential protein spots, of which seven were identified with LC-MS, including switches associated protein 70, far upstream element binding protein 1 heat shock protein 60, annexin A7, small ubiquitin-like modifier 1 activating enzyme, chaperonin-containing tail-less complex protein 1 and annexin A2. These proteins were found to be associated with proliferation apoptosis, invasion, metastasis, adhesion of gastric cancer cells with bioinformatic analysis. Western blot analysis confirmed that expressions of these proteins in BGC823 were consistent with the proteomic results Conclusion:ZNF139 gene may influence the biological behavior of gastric cancer cells in many ways by regulating multiple proteins.