肝癌是全世界癌症死亡的第三大死因。造成肝癌發展和進行的機制相當複雜且涉及了基因與表觀遺傳的調控。由於高通量技術的進步，使用此這些科技的大量資料來研究在肝癌中基因與表觀遺傳的改變成為可能。一些基因、蛋白質、miRNAs、和DNA甲機化被發現在肝癌的發展中有重要性，但這些結果缺乏了系統性的觀點來說明肝癌進行的機制。因此，藉由來自病患的mRNA、miRNA、甲基化的大量資料，我們使用了系統生物學方法以及大資料庫探勘來建構肝癌不同時期的基因與表觀遺傳網路(GENs)，此網路結合了基因調控網路(GRNs)、蛋白質交互作用網路(PPINs)、以及表觀遺傳網路。為了找出每一期最重要的核心網路，主要網路投影(PNP)的方法被使用來萃取出核心網路成員。藉由比較臨近期肝癌的訊號路徑所包含的核心網路的成員，我們研究了DNA甲基化的改變和miRNA的異常調節，造成在肝癌進行中ErbB、MAPK、TGF-beta、和JAK-STAT訊號路徑擾動的影響，透過這些路徑，外部訊號進一步的傳遞到轉錄因子(TF)而異常的調控目標基因，進一步地造成有利於肝癌進行的細胞反映，包含：細胞增生，抗凋亡、異常的細胞週期、細胞存活、和轉移。此外，基於在每一期進行中表觀遺傳網路成員，我們設計了一些藥物標靶來做為藥物設計進而防止肝癌病患的病情惡化。在第一期到第二期的肝癌中，NTK2、MYC、AKT1被選為多藥物標靶而lestaurtinib、dinaciclib和perifosine則是相對應的多藥物分子。在第二期到第三期的肝癌中，DDIT3、PDGFB和JUN被選為多藥物標靶，而celecoxib、axitinib 和vinblastine則是相對應的多藥物分子。在第三期到第四期的肝癌中，STAT3、IL1B、和NFKB1被選為多藥物標靶，而atiprimod、celastrol和bortezomib則是相對應的多藥物分子。此研究所提出的方法不僅探究了肝癌進行的分子機制，也提供了多標靶給肝癌的多藥物設計。

Hepatocellular carcinoma (HCC) is the third leading cause of cancer death worldwide. The mechanisms leading to development and progression of HCC are complicated and implicated in both genetic and epigenetic regulation. Thanks to the advance of high-throughput technologies, it becomes possible to use such technologies to investigate the genetic and epigenetic alteration in HCC with large amount of data. Some genes, proteins, miRNAs, and DNA methylation have been found important in the development of HCC, but these results are lack of a systematic view to elucidate the progression mechanisms of HCC. Therefore, with abundant data of mRNA profiles, miRNA profiles and methylation profiles from HCC patients, we used a systems biology approach and big database mining to construct genetic and epigenetic networks (GENs) that combine gene regulatory networks (GRNs), protein-protein networks (PPINs) and epigenetic network at different stages of hepatocarcinogenesis. For figuring out the most important core networks in each stage, principal network projection (PNP) is further facilitated to extract the core network markers. By comparing the pathways involved in core network biomarks between neighboring stages of HCC, we investigate how the changes of DNA methylation and aberrant regulations of miRNAs have impacts on the perturbation of ErbB, MAPK, TGF-beta, and JAK-STAT signaling pathways in the hepatocarcinogenesis, through which extracellular signals are further transduced to TFs to aberrantly regulate their target genes, resulting in favorable cellular responses for progression of HCC i.e. cell proliferation, anti-apoptosis, aberrant cell cycle, cell survival, and metastasis. Moreover, based on epigenetic network markers of each progression stage, we select several potential multiple drug targets for multiple drug design to prevent the progression for HCC patients; NTK2, MYC and AKT1 are selected as potential multiple drug targets and lestaurtinib, dinaciclib and perifosine are suggested as corresponding multiple drug molecules in HCC from stage I to stage II. DDIT3, PDGFB and JUN are selected as potential multiple drug targets and celecoxib, axitinib and vinblastine are suggested as corresponding multiple drug molecules in HCC from stage II to stage III. STAT3, IL1B and NFKB1 are selected as potential multiple drug targets and atiprimod, celastrol and bortezomib are suggested as corresponding multiple drug molecules in HCC from stage III to stage IV. The proposed method could not only investigate the progression molecular mechanisms of HCC but also provide potential multiple targets for multiple drug design of HCC.

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