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iConcept Journal of Emerging Issues in Medical Diagnosis and Treatment
Title
iConcept Journal of Emerging Issues in Medical Diagnosis and Treatment
Editor
Eugenia Giannopoulou
ISSN
2309-3528
Publisher
iConcept Press

iConcept Journal of Emerging Issues in Medical Diagnosis and Treatment

Genome-Wide Detection of Putative Oncofetal Genes in Human Hepatocellular Carcinoma by Splicing Pattern Comparison

by Chia-Hung Liu, Kuan-Ting Lin, Chi-Ying F Huang, Yih-Jyh Shann, Yu-Shi Lin, Cheng-Yan Kao and Chun-Nan Hsu

Volume: 1 (2010); Issue: 1

Abstract

Oncofetal genes are those genes that express themselves similarly in fetal and tumorous adult tissues but differently or below detectable levels in normal adult tissues. These genes are thought to play important roles in cell proliferation, differentiation and carcinogenesis. They have recently been used as biomarkers of cancer. For example, the alpha-fetoprotein (AFP) is one of the most commonly used diagnostic markers for hepatocellular carcinoma (HCC). In this paper, we present a computational method that compares the distributions of co-expression splicing patterns to detect potential biomarker genes in HCC, according to the cDNA/EST data. Using this method, we successfully identified 84 putative oncofetal genes (POFG) in HCC. We also found that the fetal and tumorous isoforms of POFG tended to be longer than their normal counterparts. Our preliminary screening of domain compositions of those long fetal/tumorous isoforms re-discovered a pleckstrin homology (PH) domain on AKT2, which is known to be cancer-related.

Author Details

Chia-Hung Liu
Graduate Institute of Biomedical Electronic and Bioinformatics, National Taiwan University, Taiwan, Taiwan
Kuan-Ting Lin
Institute of Biomedical Informatics, National Yang-Ming University, Taiwan, Taiwan
Chi-Ying F Huang
Institute of Clinical Medicine, National Yang-Ming University, Taiwan, Taiwan
Yih-Jyh Shann
Institute of Clinical Medicine, National Yang-Ming University, Taiwan, Taiwan
Yu-Shi Lin
Department of Computer Science and Information Engineering, National Taiwan University, Taiwan, Taiwan
Cheng-Yan Kao
Department of Computer Science and Information Engineering,, National Taiwan University, Taiwan, Taiwan
Chun-Nan Hsu
Institute of Information Science, Academia Sinica, Taiwan, Taiwan

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