Analyzing differential regulatory networks modulated by continuous-state genomic features in glioblastoma multiforme

Yu Chiao Chiu; Kai Wen Liang; Tzu Hung Hsiao; Yidong Chen; Eric Y. Chuang

doi:10.1109/BIBM.2015.7359676

Analyzing differential regulatory networks modulated by continuous-state genomic features in glioblastoma multiforme

Yu Chiao Chiu, Kai Wen Liang, Tzu Hung Hsiao, Yidong Chen, Eric Y. Chuang

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

1 Scopus citations

Abstract

Gene regulatory networks are a global representation of complex interactions between molecules that dictate cellular behavior. Study of a regulatory network modulated by single or multiple modulators' expression levels, including microRNAs (miRNAs) and transcription factors (TFs), in different conditions can further reveal the modulators' roles in diseases such as cancers. Existing computational methods for identifying such modulated regulatory networks are typically carried out by comparing groups of samples dichotomized with respect to the modulator status, ignoring the fact that most biological features are intrinsically continuous variables. Here we devised a sliding window-based regression scheme and proposed the Regression-based Inference of Modulation (RIM) algorithm to infer the dynamic gene regulation modulated by continuous-state modulators. We demonstrated the improvement in performance as well as computation efficiency achieved by RIM. Applying RIM to genome-wide expression profiles of 520 glioblastoma multiforme (GBM) tumors, we investigated miRNA-and TF-modulated gene regulatory networks and showed their association with dynamic cellular processes and brain-related functions in GBM. Overall, the proposed algorithm provides an efficient and robust scheme for comprehensively studying modulated gene regulatory networks.

Original language	English (US)
Title of host publication	Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015
Editors	lng. Matthieu Schapranow, Jiayu Zhou, Xiaohua Tony Hu, Bin Ma, Sanguthevar Rajasekaran, Satoru Miyano, Illhoi Yoo, Brian Pierce, Amarda Shehu, Vijay K. Gombar, Brian Chen, Vinay Pai, Jun Huan
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	171-176
Number of pages	6
ISBN (Electronic)	9781467367981
DOIs	https://doi.org/10.1109/BIBM.2015.7359676
State	Published - Dec 16 2015
Event	IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015 - Washington, United States Duration: Nov 9 2015 → Nov 12 2015

Publication series

Name	Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015

Other

Other	IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015
Country/Territory	United States
City	Washington
Period	11/9/15 → 11/12/15

Keywords

competing endogenous RNA
differential regulatory networks
gene modulation
glioblastoma multiforme
transcription factor

ASJC Scopus subject areas

Software
Artificial Intelligence
Health Informatics
Biomedical Engineering

Access to Document

10.1109/BIBM.2015.7359676

Cite this

Chiu, Y. C., Liang, K. W., Hsiao, T. H., Chen, Y., & Chuang, E. Y. (2015). Analyzing differential regulatory networks modulated by continuous-state genomic features in glioblastoma multiforme. In L. M. Schapranow, J. Zhou, X. T. Hu, B. Ma, S. Rajasekaran, S. Miyano, I. Yoo, B. Pierce, A. Shehu, V. K. Gombar, B. Chen, V. Pai, & J. Huan (Eds.), Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015 (pp. 171-176). Article 7359676 (Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBM.2015.7359676

Analyzing differential regulatory networks modulated by continuous-state genomic features in glioblastoma multiforme. / Chiu, Yu Chiao; Liang, Kai Wen; Hsiao, Tzu Hung et al.
Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015. ed. / lng. Matthieu Schapranow; Jiayu Zhou; Xiaohua Tony Hu; Bin Ma; Sanguthevar Rajasekaran; Satoru Miyano; Illhoi Yoo; Brian Pierce; Amarda Shehu; Vijay K. Gombar; Brian Chen; Vinay Pai; Jun Huan. Institute of Electrical and Electronics Engineers Inc., 2015. p. 171-176 7359676 (Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Chiu, YC, Liang, KW, Hsiao, TH, Chen, Y & Chuang, EY 2015, Analyzing differential regulatory networks modulated by continuous-state genomic features in glioblastoma multiforme. in LM Schapranow, J Zhou, XT Hu, B Ma, S Rajasekaran, S Miyano, I Yoo, B Pierce, A Shehu, VK Gombar, B Chen, V Pai & J Huan (eds), Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015., 7359676, Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015, Institute of Electrical and Electronics Engineers Inc., pp. 171-176, IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015, Washington, United States, 11/9/15. https://doi.org/10.1109/BIBM.2015.7359676

Chiu YC, Liang KW, Hsiao TH, Chen Y, Chuang EY. Analyzing differential regulatory networks modulated by continuous-state genomic features in glioblastoma multiforme. In Schapranow LM, Zhou J, Hu XT, Ma B, Rajasekaran S, Miyano S, Yoo I, Pierce B, Shehu A, Gombar VK, Chen B, Pai V, Huan J, editors, Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015. Institute of Electrical and Electronics Engineers Inc. 2015. p. 171-176. 7359676. (Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015). doi: 10.1109/BIBM.2015.7359676

Chiu, Yu Chiao ; Liang, Kai Wen ; Hsiao, Tzu Hung et al. / Analyzing differential regulatory networks modulated by continuous-state genomic features in glioblastoma multiforme. Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015. editor / lng. Matthieu Schapranow ; Jiayu Zhou ; Xiaohua Tony Hu ; Bin Ma ; Sanguthevar Rajasekaran ; Satoru Miyano ; Illhoi Yoo ; Brian Pierce ; Amarda Shehu ; Vijay K. Gombar ; Brian Chen ; Vinay Pai ; Jun Huan. Institute of Electrical and Electronics Engineers Inc., 2015. pp. 171-176 (Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015).

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abstract = "Gene regulatory networks are a global representation of complex interactions between molecules that dictate cellular behavior. Study of a regulatory network modulated by single or multiple modulators' expression levels, including microRNAs (miRNAs) and transcription factors (TFs), in different conditions can further reveal the modulators' roles in diseases such as cancers. Existing computational methods for identifying such modulated regulatory networks are typically carried out by comparing groups of samples dichotomized with respect to the modulator status, ignoring the fact that most biological features are intrinsically continuous variables. Here we devised a sliding window-based regression scheme and proposed the Regression-based Inference of Modulation (RIM) algorithm to infer the dynamic gene regulation modulated by continuous-state modulators. We demonstrated the improvement in performance as well as computation efficiency achieved by RIM. Applying RIM to genome-wide expression profiles of 520 glioblastoma multiforme (GBM) tumors, we investigated miRNA-and TF-modulated gene regulatory networks and showed their association with dynamic cellular processes and brain-related functions in GBM. Overall, the proposed algorithm provides an efficient and robust scheme for comprehensively studying modulated gene regulatory networks.",

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Analyzing differential regulatory networks modulated by continuous-state genomic features in glioblastoma multiforme

Abstract

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Keywords

ASJC Scopus subject areas

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