Introduction Traditional Chinese medicine (TCM), which originated in ancient China and has been developed for thousands of years, is widely used in China and the west nowadays as a part of complementary and alternative medicine. In order to advance the modernization of TCM, more evidence of the efficacy and pharmacological mechanisms at molecular level is still necessary for better understanding of TCM. The microarray technology can provide deep insights into the mechanisms of action at transcriptional level and is successfully applied to drug discovery and development. Based on gene expression data, a number of genes/ targets, for which the expression levels significantly changed between the biological states before and after treatment by TCM in vivo or in vitro, can be identified by various statistical algorithms and used to interpret complex therapeutic effects of TCM. Moreover, the network-based approaches have recently been proposed to systematically investigate the molecular mechanisms of TCM from a systematic point of view. This paper reviewed the TCM researches based on the microarray data as well as the network-based system biology. The discussions on the perspective of integrating the microarray technology with the network-based approaches were also given in this review. Conclusion TCM uses holistic and synergistic approaches for disease treatment and keeping the yin-yang balance of body energy. Microarray technology can monitor TCM-induced changes of whole genomics and be used to identify the differentially expressed genes for further interpretation of TCM efficacy. Further research is needed to improve our methods and understanding of TCM.
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