P42.3 gene is highly reserved in mammalian. As an oncogene, p42.3 plays an important role in the transformation process from normal gastric epithelial cell to cancer cell. Cui Y et al.  found that MiR-29a can target at p42.3 gene. The p42.3 gene silencing can change the expression of two key genes -- CHK2 and cyclin B1, which would further inhibit cell proliferation and the advances of cell cycle. The above results verify that p42.3 plays an important role in cell cycle regulation.
Based on the theory that the protein’s function is determined by its spatial structure, we found molecules similar to p42.3 protein by bioinformatic software in related databank, and then predicted the spatial structure of p42.3 protein and analyzed the structure-function relation. Threading method was adopted to predict the spatial conformation of p42.3 gene for there is no homologous protein with p42.3 at present. Analysis of the structure data indicated that EF-hand structure domain existed in the N-end of the p42.3 protein. It has been reported that this conformation exists in the S100 family. A CC domain exists in the C-end, the three-dimentional conformation of which has high homology with the CC domain in the C-end of the APC molecule amino acid (95%). Study verified that the deactivation of APC gene plays an important role in the genesis and development of GC, which indicated that p42.3 protein may interfere related cell signal transduction pathway and biological function by influencing the active site of APC protein .
In protein molecule, easily distinguishable 3D structure is folded by two or more independent structure domains [11, 12]. 3D structure exploring of protein molecule enables people to organize the rapidly growing set of thousands of known protein shapes, to identify new types of protein architecture, and to discover unexpected evolutionary relations . The measurement of protein structure similarity influences the prediction and evaluation of the protein structure . Hu min et al.  proposed a method for measuring protein structure similarity based on the molecular inner spatial density distribution, which the protein molecule space is performed concentric spherical shell division and got many shell structure space units with a certain radial depth, then the number of C atom in each spherical shell is counted. At last the spatial structure similarity of the two proteins is calculated by similarity calculation function. Zou BJ et al.  proposed a new method for measuring protein structure similarity based on spatial density characteristic, which is regarding spatial spherical polar coordinate as the presentation model. The model based on spherical polar coordinate can provide theoretical basis for protein classification and protein function prediction. We transfer the protein 3D structure information into distance sequence information which is then performed fast Fourier transform, and the spatial domain information of protein structure is transformed into frequency domain information. At last, the similarity of spatial domain information is determined by the similarity of frequency domain information .
The construction of gene regulatory network is based on the gene expression data with every gene as a random variable and the expression level in different conditions as its value. Moreover, gene regulatory network is sparsity , which means, one a few genes directly affect the transcription process. Having the characteristic of illustrating the probability dependence of variables in the form of possibility, Bayesian Network is very suitable for analyzing and predicting this kind of sparse network.
Based on the two characteristic structures (EF-hand structure domain and CC domain) of p42.3 protein, we collected a large amount of similar protein. The similar protein set was screened by protein structure similarity comparison method based on spherical polar coordinate. The constructed regulatory network was optimized by Bayesian Network in order to obtain the optimal regulatory pathway. The possible action way of p42.3 gene in tumorigenesis was explored, which provided powerful means for the further study on mechanism of action. Applying mathematics and computer technolgoy in protein structure prediction and function analysis is a new trend in the field of biomedical research.