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Open Access Research

p42.3 gene expression in gastric cancer cell and its protein regulatory network analysis

Jianhua Zhang1, Chunlei Lu2, Zhigang Shang1, Rui Xing3, Li Shi1* and Youyong Lv3*

Author Affiliations

1 Department of Biomedical Engineering, School of Electrical Engineering, Zhengzhou University, Zhengzhou, Henan Province, 450001, China

2 Department of Gastrointestinal Surgery, PLA No.101Hospital, No.101, North Xingyuan Road, Wuxi, Jiangsu Province, 214044, China

3 Laboratory of Molecular Oncology, Beijing Institute for Cancer Research, School of Oncology, Peking University, Beijing, Hai-Dian District, 100080, China

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Theoretical Biology and Medical Modelling 2012, 9:53  doi:10.1186/1742-4682-9-53

Published: 11 December 2012

Abstract

Background

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 then to obtain the optimal regulatory pathway.

Methods

The 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.

Conclusion

It 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.

Keywords:
p42.3; Gastric cancer; Protein structure; Bayesian regulatory network