In silico identification of oncogenic potential of fyn-related kinase in hepatocellular carcinoma

Jia Shing Chen, Wei Shiang Hung, Hsiang Han Chan, Shaw Jenq Tsai, H. Sunny Sun

研究成果: Article

94 引文 (Scopus)

摘要

Motivation: Cancer development is a complex and heterogeneous process. It is estimated that 5-10% of human genes probably contribute to oncogenesis, whereas current experimentally validated cancer genes only cover 1% of the human genome. Thus hundreds of cancer genes may still remain to be identified. To search for new genes that play roles in carcinogenesis and facilitate cancer research, we developed a systematic workflow to use information saved in a previously established tumor-associated gene (TAG) database.Results: By exploiting the information of conserved protein domains from the TAG, we identified 183 potential new TAGs. As a proof-of-concept, one predicted oncogene, fyn-related kinase (FRK), which shows an aberrant digital expression pattern in liver cancer cells, was selected for further investigation. Using 68 paired hepatocellular carcinoma samples, we found that FRK was up-regulated in 52% of cases (P < 0.001). Tumorigenic assays performed in Hep3B and HepG2 cell lines revealed a significant correlation between the level of FRK expression and invasiveness, suggesting that FRK is a positive regulator of invasiveness in liver cancer cells.Conclusion: These findings implied that FRK is a multitalented signal transduction molecule that produces diverse biological responses in different cell types in various microenvironments. In addition, our data demonstrated the accuracy of computational prediction and suggested that other predicted TAGs can be potential targets for future cancer research.Availability: The TAG database is available online at the Bioinformatics Center website: http://www.binfo.ncku.edu.tw/TAG/.

原文English
頁(從 - 到)420-427
頁數8
期刊Bioinformatics
29
發行號4
DOIs
出版狀態Published - 2013 二月 15

指紋

Computer Simulation
Hepatocellular Carcinoma
Phosphotransferases
Genes
Cancer
Gene
Tumor
Neoplasms
Tumors
Neoplasm Genes
Liver Neoplasms
Cell
Cells
Carcinogenesis
Liver
Databases
Workflow
Hep G2 Cells
Human Genome
Signal Transduction

All Science Journal Classification (ASJC) codes

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

引用此文

Chen, Jia Shing ; Hung, Wei Shiang ; Chan, Hsiang Han ; Tsai, Shaw Jenq ; Sunny Sun, H. / In silico identification of oncogenic potential of fyn-related kinase in hepatocellular carcinoma. 於: Bioinformatics. 2013 ; 卷 29, 編號 4. 頁 420-427.
@article{f095d58133f74b0e85fb69cd030dca16,
title = "In silico identification of oncogenic potential of fyn-related kinase in hepatocellular carcinoma",
abstract = "Motivation: Cancer development is a complex and heterogeneous process. It is estimated that 5-10{\%} of human genes probably contribute to oncogenesis, whereas current experimentally validated cancer genes only cover 1{\%} of the human genome. Thus hundreds of cancer genes may still remain to be identified. To search for new genes that play roles in carcinogenesis and facilitate cancer research, we developed a systematic workflow to use information saved in a previously established tumor-associated gene (TAG) database.Results: By exploiting the information of conserved protein domains from the TAG, we identified 183 potential new TAGs. As a proof-of-concept, one predicted oncogene, fyn-related kinase (FRK), which shows an aberrant digital expression pattern in liver cancer cells, was selected for further investigation. Using 68 paired hepatocellular carcinoma samples, we found that FRK was up-regulated in 52{\%} of cases (P < 0.001). Tumorigenic assays performed in Hep3B and HepG2 cell lines revealed a significant correlation between the level of FRK expression and invasiveness, suggesting that FRK is a positive regulator of invasiveness in liver cancer cells.Conclusion: These findings implied that FRK is a multitalented signal transduction molecule that produces diverse biological responses in different cell types in various microenvironments. In addition, our data demonstrated the accuracy of computational prediction and suggested that other predicted TAGs can be potential targets for future cancer research.Availability: The TAG database is available online at the Bioinformatics Center website: http://www.binfo.ncku.edu.tw/TAG/.",
author = "Chen, {Jia Shing} and Hung, {Wei Shiang} and Chan, {Hsiang Han} and Tsai, {Shaw Jenq} and {Sunny Sun}, H.",
year = "2013",
month = "2",
day = "15",
doi = "10.1093/bioinformatics/bts715",
language = "English",
volume = "29",
pages = "420--427",
journal = "Bioinformatics",
issn = "1367-4803",
publisher = "Oxford University Press",
number = "4",

}

In silico identification of oncogenic potential of fyn-related kinase in hepatocellular carcinoma. / Chen, Jia Shing; Hung, Wei Shiang; Chan, Hsiang Han; Tsai, Shaw Jenq; Sunny Sun, H.

於: Bioinformatics, 卷 29, 編號 4, 15.02.2013, p. 420-427.

研究成果: Article

TY - JOUR

T1 - In silico identification of oncogenic potential of fyn-related kinase in hepatocellular carcinoma

AU - Chen, Jia Shing

AU - Hung, Wei Shiang

AU - Chan, Hsiang Han

AU - Tsai, Shaw Jenq

AU - Sunny Sun, H.

PY - 2013/2/15

Y1 - 2013/2/15

N2 - Motivation: Cancer development is a complex and heterogeneous process. It is estimated that 5-10% of human genes probably contribute to oncogenesis, whereas current experimentally validated cancer genes only cover 1% of the human genome. Thus hundreds of cancer genes may still remain to be identified. To search for new genes that play roles in carcinogenesis and facilitate cancer research, we developed a systematic workflow to use information saved in a previously established tumor-associated gene (TAG) database.Results: By exploiting the information of conserved protein domains from the TAG, we identified 183 potential new TAGs. As a proof-of-concept, one predicted oncogene, fyn-related kinase (FRK), which shows an aberrant digital expression pattern in liver cancer cells, was selected for further investigation. Using 68 paired hepatocellular carcinoma samples, we found that FRK was up-regulated in 52% of cases (P < 0.001). Tumorigenic assays performed in Hep3B and HepG2 cell lines revealed a significant correlation between the level of FRK expression and invasiveness, suggesting that FRK is a positive regulator of invasiveness in liver cancer cells.Conclusion: These findings implied that FRK is a multitalented signal transduction molecule that produces diverse biological responses in different cell types in various microenvironments. In addition, our data demonstrated the accuracy of computational prediction and suggested that other predicted TAGs can be potential targets for future cancer research.Availability: The TAG database is available online at the Bioinformatics Center website: http://www.binfo.ncku.edu.tw/TAG/.

AB - Motivation: Cancer development is a complex and heterogeneous process. It is estimated that 5-10% of human genes probably contribute to oncogenesis, whereas current experimentally validated cancer genes only cover 1% of the human genome. Thus hundreds of cancer genes may still remain to be identified. To search for new genes that play roles in carcinogenesis and facilitate cancer research, we developed a systematic workflow to use information saved in a previously established tumor-associated gene (TAG) database.Results: By exploiting the information of conserved protein domains from the TAG, we identified 183 potential new TAGs. As a proof-of-concept, one predicted oncogene, fyn-related kinase (FRK), which shows an aberrant digital expression pattern in liver cancer cells, was selected for further investigation. Using 68 paired hepatocellular carcinoma samples, we found that FRK was up-regulated in 52% of cases (P < 0.001). Tumorigenic assays performed in Hep3B and HepG2 cell lines revealed a significant correlation between the level of FRK expression and invasiveness, suggesting that FRK is a positive regulator of invasiveness in liver cancer cells.Conclusion: These findings implied that FRK is a multitalented signal transduction molecule that produces diverse biological responses in different cell types in various microenvironments. In addition, our data demonstrated the accuracy of computational prediction and suggested that other predicted TAGs can be potential targets for future cancer research.Availability: The TAG database is available online at the Bioinformatics Center website: http://www.binfo.ncku.edu.tw/TAG/.

UR - http://www.scopus.com/inward/record.url?scp=84874338100&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84874338100&partnerID=8YFLogxK

U2 - 10.1093/bioinformatics/bts715

DO - 10.1093/bioinformatics/bts715

M3 - Article

C2 - 23267173

AN - SCOPUS:84874338100

VL - 29

SP - 420

EP - 427

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

IS - 4

ER -