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

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

• Kang SH
• Park JA
• Hong SS
• Kim KW

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

MeSH Terms

Angiogenesis Inducing Agents
Anoxia
Carcinoma, Hepatocellular*
Computational Biology
Computer Simulation*
Factor XII
Humans*
Oligonucleotide Array Sequence Analysis
Osteopontin
Angiogenesis Inducing Agents
Factor XII
Osteopontin