Genomics Inform.  2004 Sep;2(3):134-141.

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

Affiliations
  • 1College of Pharmacy and Research Institute of Pharmaceutical Sciences,Seoul National University,Seoul 151-742, Korea. qwonkim@plaza.snu.ac.kr
  • 2Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-742,Korea.

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 anti-angiogenic factor. Collectively, we suggest that using a combination of in silico prediction and experimental approaches, we can identify HCC-specific angiogenesis-related factors effectively and rapidly.

Keyword

HCC; hepatocellular carcinoma; bioinformatics; angiogenesis; hmmer; blast
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