In silico Prediction of Angiogenesis-related Genes in Human Hepatocellular Carcinoma.
- Author:
Seung Hui KANG
1
;
Jeong Ae PARK
;
Soon Sun HONG
;
Kyu Won KIM
Author Information
1. College of Pharmacy and Research Institute of Pharmaceutical Sciences,Seoul National University,Seoul 151-742, Korea. qwonkim@plaza.snu.ac.kr
- Publication Type:Original Article
- Keywords:
HCC;
hepatocellular carcinoma;
bioinformatics;
angiogenesis;
hmmer;
blast
- MeSH:
Angiogenesis Inducing Agents;
Anoxia;
Carcinoma, Hepatocellular*;
Computational Biology;
Computer Simulation*;
Factor XII;
Humans*;
Oligonucleotide Array Sequence Analysis;
Osteopontin
- From:Genomics & Informatics
2004;2(3):134-141
- CountryRepublic of Korea
- Language:English
-
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.
