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Applying NGS Data to Find Evolutionary Network Biomarkers from the Early and Late Stages of Hepatocellular Carcinoma.
| Content Provider | Europe PMC |
|---|---|
| Author | Wong, Yung-Hao Wu, Chia-Chou Lin, Chih-Lung Chen, Ting-Shou Chang, Tzu-Hao Chen, Bor-Sen |
| Copyright Year | 2015 |
| Abstract | Hepatocellular carcinoma (HCC) is a major liver tumor (~80%), besides hepatoblastomas, angiosarcomas, and cholangiocarcinomas. In this study, we used a systems biology approach to construct protein-protein interaction networks (PPINs) for early-stage and late-stage liver cancer. By comparing the networks of these two stages, we found that the two networks showed some common mechanisms and some significantly different mechanisms. To obtain differential network structures between cancer and noncancer PPINs, we constructed cancer PPIN and noncancer PPIN network structures for the two stages of liver cancer by systems biology method using NGS data from cancer cells and adjacent noncancer cells. Using carcinogenesis relevance values (CRVs), we identified 43 and 80 significant proteins and their PPINs (network markers) for early-stage and late-stage liver cancer. To investigate the evolution of network biomarkers in the carcinogenesis process, a primary pathway analysis showed that common pathways of the early and late stages were those related to ordinary cancer mechanisms. A pathway specific to the early stage was the mismatch repair pathway, while pathways specific to the late stage were the spliceosome pathway, lysine degradation pathway, and progesterone-mediated oocyte maturation pathway. This study provides a new direction for cancer-targeted therapies at different stages. |
| ISSN | 23146133 |
| Journal | Biomed Research International |
| Volume Number | 2015 |
| PubMed Central reference number | PMC4558430 |
| PubMed reference number | 26366411 |
| e-ISSN | 23146141 |
| DOI | 10.1155/2015/391475 |
| Language | English |
| Publisher | Hindawi |
| Publisher Date | 2015-08-20 |
| Access Restriction | Open |
| Rights License | This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Copyright © 2015 Yung-Hao Wong et al. |
| Content Type | Text |
| Resource Type | Article |
| Subject | Immunology and Microbiology Medicine Biochemistry, Genetics and Molecular Biology |
