The Study Of Traditional Chinese Medicine Mechanism Based On Gene Co-expression Modules

As part of our splendid national culture, Chinese medicine has a long history and great achievements. But as a discipline, because of obscure theory and controversial mechanism, Chinese medicine is difficult to be recognized by modern science. Therefore, for a better future, we should use scientific methods to research the theory and function mechanism of traditional Chinese medicine. In the present study the mechanism of traditional Chinese medicine approaches, gene chip technology has advantages of high-throughput and simple operation, can quickly locate specific expression of certain genes, so researchers can have a preliminary understanding about the complex mechanism of traditional Chinese medicine, which indicates the direction for further study. However, the conventional method of microarray data analysis can’t make the most of information, and can’t fully tap the local expression information. Biclustering analysis can find subsets with expression of universal (ie gene co-expression module) from two directions (gene and samples), can well reflect the local characteristics of microarray data, so the complexity of the mechanism of action of Chinese medicine can be decomposed multiple independent gene co-expression modules, through the analysis of these function modules can give us a comprehensive understanding of the mechanism of Chinese medicine.The Si-Wu-Tang formula is composed of four herbs, Radix Rehmanniae praeparata, Radix Angelicae Sinensis, Rhizoma Ligustici Chuanxiong and Radix Paeoniae Alba, is a classic prescription for gynecological blood and regulate menstruation, also has antioxidant, promoting blood circulation effect; shikonin is the main active component of Lithospermum erythrorhizon, has effects of anti-inflammatory sterilization, anti-tumor and treatment of burn, scald and various skin disease. This study integrates the microarray data of cMap database and Si-Wu-Tang gene chip and shikonin gene chip, using FABIA algorithm analysis for Si-Wu-Tang-cMap and shikonin-cMap data matrix, after biclustering analysis, we get48and49gene co-expression modules respectively. The biological functions of each module were defined GO and KEGG enrichment, and then according to the gene co-expression modules sample molecules are involved, we obtain the molecular module expression profile, and calculated the Tanimoto similarity between any two sample molecules.Based on the analysis of Si-Wu-Tang gene co-expression modules, we found56similar small molecules with Si-Wu-Tang in genes expression activity and predicted49potential targets, suggesting that Si-Wu-Tang may play a role of estrogen by regulate the endocrine activity mediated by the central nervous system; Si-Wu-Tang antioxidant activity may be associated with Nrf2-ARE antioxidant pathway; blood stasis effect might be affected by the efficacy of GABA and epinephrine on the two-way adjustment of renin-angiotensin system; the hemostatic mechanism of Si-Wu-Tang may be related to the activity of vitamin K, and the inhibition of uterine contraction mechanism may be closely related with BKCa channel. Through the gene co-expression modules analysis of Shikonin, we found8Shikonin similar moleculars, predicted11Shikonin’s potential targets, suggesting that Shikonin may share the same mechanism of hepatoprotective with chenodeoxycholic acid; shikonin vasodilating effects may be similar with hydralazine; mechanism of Lithospermum oil for treating burn and scald may because of shikonin has similar biological activity with retinoic acid, can regulate cell differentiation and promote tissue regeneration and wound healing.