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BioMed Research International
Volume 2016, Article ID 1035945, 6 pages
Research Article

Modeling Gene Regulation in Liver Hepatocellular Carcinoma with Random Forests

Department of Computer Engineering, Faculty of Engineering, Antalya International University, Antalya, Turkey

Received 18 May 2016; Accepted 21 September 2016

Academic Editor: Anton M. Jetten

Copyright © 2016 Hilal Kazan. 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.


Liver hepatocellular carcinoma (HCC) remains a leading cause of cancer-related death. Poor understanding of the mechanisms underlying HCC prevents early detection and leads to high mortality. We developed a random forest model that incorporates copy-number variation, DNA methylation, transcription factor, and microRNA binding information as features to predict gene expression in HCC. Our model achieved a highly significant correlation between predicted and measured expression of held-out genes. Furthermore, we identified potential regulators of gene expression in HCC. Many of these regulators have been previously found to be associated with cancer and are differentially expressed in HCC. We also evaluated our predicted target sets for these regulators by making comparison with experimental results. Lastly, we found that the transcription factor E2F6, one of the candidate regulators inferred by our model, is predictive of survival rate in HCC. Results of this study will provide directions for future prospective studies in HCC.