Bioinformatics and gene chip are two new technologies in the field of life science. Bioinformatics is very important to the data analysis of gene chip. The expression and regulation of gene have a profound influence on progression and metastasis of malignant tumors. In the present report, the oligonucleotide microarray technique was used to identify gene expression profiling and screen differential expression genes in breast cancer with a special emphasis on metastasis factors. Then a linear differential model is employed to construct rough genetic regulatory network of gene related to breast cancer metastasis. An available gene chip system was used to analyze surgical samples, including both breast cancer primary tissue and metastasis tissue, collected from 30 patients in different clinical staging. 27 differential expression genes were identified. 14 of the total are up-regulation genes whose Ratio is large for 3, and the rest are down-regulation gene whose Ratio is small for 0.33. In search of putative metastasis and tumor progression factors with Bioinformatics method, linear differential model, a linear model estimated -by Lest Squares Method, was used to construct rough regulatory network of gene related to breast cancer metastasis. With the analysis of the rough regulatory network constructed by the linear differential model, the reliability of regulatory network and abnormality of signal transmission pathways caused by multiple gene abnormal expression, which maybe correlate to breast cancer metastasis, were manifested.