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In silica Prediction of Angiogenesis-related Genes in Human Hepatocellular Carcinoma  

Kang, Seung-Hui (College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Interdisciplinary Program in Bioinformatics, Seoul National University)
Park, Jeong-Ae (College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University)
Hong, Soon-Sun (College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University)
Kim, Kyu-Won (College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Interdisciplinary Program in Bioinformatics, Seoul National University)
Publication Information
Genomics & Informatics / v.2, no.3, 2004 , pp. 134-141 More about this Journal
Abstract
Hepatocellular carcinoma (HCC) is one of the most common malignancies worldwide and a typical hypervascular tumor. Therefore, it is important to find factors related to angiogenesis in the process of HCC malignancy. In order to find angiogenesis-related factors in HCC, we used combined methods of in silico prediction and an experimental assay. We analyzed 1457 genes extracted from cDNA microarray of HCC patients by text-mining, sequence similarity search and domain analysis. As a result, we predicted that 16 genes were likely to be involved in angiogenesis and then the effects of these genes were confirmed by hypoxia response element(HRE)-luciferase assay. For instant, we classified osteopontin into a potent angiogenic factor and coagulation factor XII into a significant anti­angiogenic factor. Collectively, we suggest that using a combination of in silico prediction and experimental approaches, we can identify HCC-specific angiogenesis­related factors effectively and rapidly.
Keywords
HCC; hepatocellular carcinoma; bioinformatics; angiogenesis; hmmer; blast;
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