P42.3 gene expression in gastric cancer cell and its protein regulatory network analysis

Jianhua Zhang,Zhigang Shang,Li Shi,Chunlei Lu,Youyong Lv,Rui Xing

doi:10.1186/1742-4682-9-53

Abstract

BackgroundTo analyze the p42.3 gene expression in gastric cancer (GC) cell, find the relationship between protein structure and function, establish the regulatory network of p42.3 protein molecule and then to obtain the optimal regulatory pathway.MethodsThe expression of p42.3 gene was analyzed by RT-PCR, Western Blot and other biotechnologies. The relationship between the spatial conformation of p42.3 protein molecule and its function was analyzed using bioinformatics, MATLAB and related knowledge about protein structure and function. Furthermore, based on similarity algorithm of spatial layered spherical coordinate, we compared p42.3 molecule with several similar structured proteins which are known for the function, screened the characteristic nodes related to tumorigenesis and development, and established the multi variable relational model between p42.3 protein expression, cell cycle regulation and biological characteristics in the level of molecular regulatory networks. Finally, the optimal regulatory network was found by using Bayesian network.Results(1) The expression amount of p42.3 in G1 and M phase was higher than that in S and G2 phase; (2) The space coordinate systems of different structural domains of p42.3 protein were established in Matlab7.0 software; (3) The optimal pathway of p42.3 gene in protein regulatory network in gastric cancer is Ras protein, Raf-1 protein, MEK, MAPK kinase, MAPK, tubulin, spindle protein, centromere protein and tumor.ConclusionIt is of vital significance for mechanism research to find out the action pathway of p42.3 in protein regulatory network, since p42.3 protein plays an important role in the generation and development of GC.

Highlights

Gastric cancer (GC) is one of the most common malignant tumors in China and in the world
Detection results of mRNA expression RT-PCR results indicated that p42.3 exists in most of the gastric cancer (GC) cells
In the selected 12 GC cell lines, p42.3 expression cannot be detected only in SNU5, SNU16 and RF1 cell lines (Figure 1); when BGC823 cells were synchronized to different cell cycles, results demonstrated that p42.3 expression in G1 and M phases was higher than that in S and G2 phases (Figure 2)

Summary

Introduction

Gastric cancer (GC) is one of the most common malignant tumors in China and in the world. Data showed that the new increasing GC patients are more than one million annually, with China accounts for 42%. About 0.8 million people dead of GC and 44% of them are in China. As one of the high GC incidence rate and death rate countries, the morbidity and mortality of China are more than twice of the world average level [1]. The tumorigenesis and development of GC is a complex issue involving genetic variation. Existing studies have demonstrated that genes, such as erbB-2, c-met, p53, cadherin, APC and RUNX3 gene, may be involved in the development and progression of GC [2,3]. To analyze the p42.3 gene expression in gastric cancer (GC) cell, find the relationship between protein structure and function, establish the regulatory network of p42.3 protein molecule and to obtain the optimal regulatory pathway

Methods

Results

Conclusion