Reconstructing dynamic gene regulatory network for the development process of hepatocellular carcinoma

Hailong Zhu; R. Shyama Prasad Rao; Luonan Chen

doi:10.1109/BIBMW.2012.6470298

Reconstructing dynamic gene regulatory network for the development process of hepatocellular carcinoma

Hailong Zhu^*
, R. Shyama Prasad Rao
, Luonan Chen

^*Corresponding author for this work

Department of Computer Science

Research output: Chapter in book/report/conference proceeding › Conference proceeding › peer-review

2 Citations (Scopus)

Abstract

A crucial work of investigating the mechanisms of cancer development is to unraveling the dynamic nature of gene regulation during the disease process. However, reconstruction of dynamic gene regulatory network requires time-sequence samples of a biological process, which are not available for many bio-medical problems. In this paper, we propose a dynamic cascaded method to reconstruct dynamic gene networks from sample-based transcriptional data. Our method is based on two biologically plausible assumptions, which can characterise the dynamic and continuous nature of gene transcription. Our approach was successfully applied to reconstruct the dynamic gene networks of hepatocellular carcinoma (HCC) progression. The derived HCC networks were verified by functional analysis and network enrichment analysis.

Original language	English
Title of host publication	Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012
Pages	159-165
Number of pages	7
DOIs	https://doi.org/10.1109/BIBMW.2012.6470298
Publication status	Published - 2012
Event	2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012 - Philadelphia, PA, United States Duration: 4 Oct 2012 → 7 Oct 2012

Publication series

Name	Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012

Conference

Conference	2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012
Country/Territory	United States
City	Philadelphia, PA
Period	4/10/12 → 7/10/12

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

User-Defined Keywords

dynamic network
Gene regulatory network
Herpatocellulur Carcinoma
sample-based transcriptional data

Access to Document

10.1109/BIBMW.2012.6470298

Cite this

Zhu, H., Rao, R. S. P., & Chen, L. (2012). Reconstructing dynamic gene regulatory network for the development process of hepatocellular carcinoma. In Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012 (pp. 159-165). Article 6470298 (Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012). https://doi.org/10.1109/BIBMW.2012.6470298

Zhu, Hailong ; Rao, R. Shyama Prasad ; Chen, Luonan. / Reconstructing dynamic gene regulatory network for the development process of hepatocellular carcinoma. Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012. 2012. pp. 159-165 (Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012).

@inproceedings{f87a7f2ae2d94c4ca7397b0b23ca85a6,

title = "Reconstructing dynamic gene regulatory network for the development process of hepatocellular carcinoma",

abstract = "A crucial work of investigating the mechanisms of cancer development is to unraveling the dynamic nature of gene regulation during the disease process. However, reconstruction of dynamic gene regulatory network requires time-sequence samples of a biological process, which are not available for many bio-medical problems. In this paper, we propose a dynamic cascaded method to reconstruct dynamic gene networks from sample-based transcriptional data. Our method is based on two biologically plausible assumptions, which can characterise the dynamic and continuous nature of gene transcription. Our approach was successfully applied to reconstruct the dynamic gene networks of hepatocellular carcinoma (HCC) progression. The derived HCC networks were verified by functional analysis and network enrichment analysis.",

keywords = "dynamic network, Gene regulatory network, Herpatocellulur Carcinoma, sample-based transcriptional data",

author = "Hailong Zhu and Rao, \{R. Shyama Prasad\} and Luonan Chen",

year = "2012",

doi = "10.1109/BIBMW.2012.6470298",

language = "English",

isbn = "9781467327466",

series = "Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012",

pages = "159--165",

booktitle = "Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012",

note = "2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012 ; Conference date: 04-10-2012 Through 07-10-2012",

}

Zhu, H, Rao, RSP & Chen, L 2012, Reconstructing dynamic gene regulatory network for the development process of hepatocellular carcinoma. in Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012., 6470298, Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012, pp. 159-165, 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012, Philadelphia, PA, United States, 4/10/12. https://doi.org/10.1109/BIBMW.2012.6470298

Reconstructing dynamic gene regulatory network for the development process of hepatocellular carcinoma. / Zhu, Hailong; Rao, R. Shyama Prasad; Chen, Luonan.
Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012. 2012. p. 159-165 6470298 (Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012).

Research output: Chapter in book/report/conference proceeding › Conference proceeding › peer-review

TY - GEN

T1 - Reconstructing dynamic gene regulatory network for the development process of hepatocellular carcinoma

AU - Zhu, Hailong

AU - Rao, R. Shyama Prasad

AU - Chen, Luonan

PY - 2012

Y1 - 2012

N2 - A crucial work of investigating the mechanisms of cancer development is to unraveling the dynamic nature of gene regulation during the disease process. However, reconstruction of dynamic gene regulatory network requires time-sequence samples of a biological process, which are not available for many bio-medical problems. In this paper, we propose a dynamic cascaded method to reconstruct dynamic gene networks from sample-based transcriptional data. Our method is based on two biologically plausible assumptions, which can characterise the dynamic and continuous nature of gene transcription. Our approach was successfully applied to reconstruct the dynamic gene networks of hepatocellular carcinoma (HCC) progression. The derived HCC networks were verified by functional analysis and network enrichment analysis.

AB - A crucial work of investigating the mechanisms of cancer development is to unraveling the dynamic nature of gene regulation during the disease process. However, reconstruction of dynamic gene regulatory network requires time-sequence samples of a biological process, which are not available for many bio-medical problems. In this paper, we propose a dynamic cascaded method to reconstruct dynamic gene networks from sample-based transcriptional data. Our method is based on two biologically plausible assumptions, which can characterise the dynamic and continuous nature of gene transcription. Our approach was successfully applied to reconstruct the dynamic gene networks of hepatocellular carcinoma (HCC) progression. The derived HCC networks were verified by functional analysis and network enrichment analysis.

KW - dynamic network

KW - Gene regulatory network

KW - Herpatocellulur Carcinoma

KW - sample-based transcriptional data

UR - https://www.scopus.com/pages/publications/84875592916

U2 - 10.1109/BIBMW.2012.6470298

DO - 10.1109/BIBMW.2012.6470298

M3 - Conference proceeding

AN - SCOPUS:84875592916

SN - 9781467327466

T3 - Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012

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EP - 165

BT - Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012

T2 - 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012

Y2 - 4 October 2012 through 7 October 2012

ER -

Zhu H, Rao RSP, Chen L. Reconstructing dynamic gene regulatory network for the development process of hepatocellular carcinoma. In Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012. 2012. p. 159-165. 6470298. (Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012). doi: 10.1109/BIBMW.2012.6470298

Reconstructing dynamic gene regulatory network for the development process of hepatocellular carcinoma

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