Traditional Chinese medicine (TCM) treatment is regarded as a safe and effective method for many diseases. In this study, the characteristics among excessive, excessive-deficient, and deficient syndromes of Hepatocellular carcinoma (HCC) were studied using miRNA array data. We first calculated the differentially expressed miRNAs based on random module t-test and classified three TCM syndromes of HCC using SVM method. Then, the weighted miRNA-target networks were constructed for different TCM syndromes using predicted miRNA targets. Subsequently, the prioritized target genes of upexpression network of TCM syndromes were analyzed using DAVID online analysis. The results showed that there are distinctly different hierarchical cluster and network structure of TCM syndromes in HCC, but the excessive-deficient combination syndrome is extrinsically close to deficient syndrome. GO and pathway analysis revealed that the molecular mechanisms of excessive-deficient and deficient syndromes of HCC are more complex than excessive syndrome. Furthermore, although excessive-deficient and deficient syndromes have similar complex mechanisms, excessive-deficient syndrome is more involved than deficient syndrome in development of cancer process. This study suggested that miRNAs might be important mediators involved in the changing process from excessive to deficient syndromes and could be potential molecular markers for the diagnosis of TCM syndromes in HCC. 1. Introduction Hepatocellular carcinoma (HCC) is one of the most common devastating cancer types, ranking sixth in incidence, and the third leading cause of cancer related deaths worldwide [1, 2]. The hepatitis B and hepatitis C infections, idiopathic cirrhosis, and alcoholic liver diseases usually are major risk factors for HCC [3]. For early diagnosis of HCC is difficult, and more than half of the HCC patients are diagnosed too late to benefit from the curative therapies. Furthermore, molecular approaches have revealed many molecular events associated with HCC, yet molecular mechanism of cell proliferation and effective biological markers for driving hepatocarcinogenesis remain largely unknown [4]. Under these circumstances, many failing patients seek to get help from complementary and alternative medicine, especially traditional Chinese medicine (TCM). TCM is an ancient Chinese medicine that evolved through at least three thousand years of uninterrupted clinical practice. The TCM treatment usually uses a traditional diagnosis method to classify the TCM syndromes, which based on clinical symptoms and signs, followed
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