Uncover cooperative gene regulations by microRNAs and transcription factors in glioblastoma using a nonnegative hybrid factor model

Jia Meng; Hung I. Chen; Jianqiu Zhang; Yidong Chen; Yufei Huang

doi:10.1109/ICASSP.2011.5947732

Uncover cooperative gene regulations by microRNAs and transcription factors in glioblastoma using a nonnegative hybrid factor model

Jia Meng, Hung I. Chen, Jianqiu Zhang, Yidong Chen, Yufei Huang

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

6 Scopus citations

Abstract

Transcriptional regulation by transcription factors (TFs) and microRNAs controls when and how much RNA is created. Due to technical limitations, the protein level expressions of TFs are usually unknown, making computational reconstruction of transcriptional network a difficult task. We proposed here a novel Bayesian nonnegative hybrid factor model for transcriptional network modeling, which is capable to estimate both the non-negative abundances of the transcription factors, the regulatory effects of TFs and microRNAs, and the sample clustering information by integrating microarray data and existing knowledge regarding TFs and microRNAs regulated target genes. The results demonstrated its validity and effectiveness to reconstructing transcriptional networks through simulated systems and real data.

Original language	English (US)
Title of host publication	2011 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2011 - Proceedings
Pages	6012-6015
Number of pages	4
DOIs	https://doi.org/10.1109/ICASSP.2011.5947732
State	Published - 2011
Event	36th IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2011 - Prague, Czech Republic Duration: May 22 2011 → May 27 2011

Publication series

Name	ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings
ISSN (Print)	1520-6149

Other

Other	36th IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2011
Country/Territory	Czech Republic
City	Prague
Period	5/22/11 → 5/27/11

ASJC Scopus subject areas

Software
Signal Processing
Electrical and Electronic Engineering

Access to Document

10.1109/ICASSP.2011.5947732

Cite this

Meng, J., Chen, H. I., Zhang, J., Chen, Y., & Huang, Y. (2011). Uncover cooperative gene regulations by microRNAs and transcription factors in glioblastoma using a nonnegative hybrid factor model. In 2011 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2011 - Proceedings (pp. 6012-6015). Article 5947732 (ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings). https://doi.org/10.1109/ICASSP.2011.5947732

Uncover cooperative gene regulations by microRNAs and transcription factors in glioblastoma using a nonnegative hybrid factor model. / Meng, Jia; Chen, Hung I.; Zhang, Jianqiu et al.
2011 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2011 - Proceedings. 2011. p. 6012-6015 5947732 (ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings).

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

Meng, J, Chen, HI, Zhang, J, Chen, Y & Huang, Y 2011, Uncover cooperative gene regulations by microRNAs and transcription factors in glioblastoma using a nonnegative hybrid factor model. in 2011 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2011 - Proceedings., 5947732, ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings, pp. 6012-6015, 36th IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2011, Prague, Czech Republic, 5/22/11. https://doi.org/10.1109/ICASSP.2011.5947732

Meng J, Chen HI, Zhang J, Chen Y, Huang Y. Uncover cooperative gene regulations by microRNAs and transcription factors in glioblastoma using a nonnegative hybrid factor model. In 2011 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2011 - Proceedings. 2011. p. 6012-6015. 5947732. (ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings). doi: 10.1109/ICASSP.2011.5947732

Meng, Jia ; Chen, Hung I. ; Zhang, Jianqiu et al. / Uncover cooperative gene regulations by microRNAs and transcription factors in glioblastoma using a nonnegative hybrid factor model. 2011 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2011 - Proceedings. 2011. pp. 6012-6015 (ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings).

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abstract = "Transcriptional regulation by transcription factors (TFs) and microRNAs controls when and how much RNA is created. Due to technical limitations, the protein level expressions of TFs are usually unknown, making computational reconstruction of transcriptional network a difficult task. We proposed here a novel Bayesian nonnegative hybrid factor model for transcriptional network modeling, which is capable to estimate both the non-negative abundances of the transcription factors, the regulatory effects of TFs and microRNAs, and the sample clustering information by integrating microarray data and existing knowledge regarding TFs and microRNAs regulated target genes. The results demonstrated its validity and effectiveness to reconstructing transcriptional networks through simulated systems and real data.",

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AB - Transcriptional regulation by transcription factors (TFs) and microRNAs controls when and how much RNA is created. Due to technical limitations, the protein level expressions of TFs are usually unknown, making computational reconstruction of transcriptional network a difficult task. We proposed here a novel Bayesian nonnegative hybrid factor model for transcriptional network modeling, which is capable to estimate both the non-negative abundances of the transcription factors, the regulatory effects of TFs and microRNAs, and the sample clustering information by integrating microarray data and existing knowledge regarding TFs and microRNAs regulated target genes. The results demonstrated its validity and effectiveness to reconstructing transcriptional networks through simulated systems and real data.

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Uncover cooperative gene regulations by microRNAs and transcription factors in glioblastoma using a nonnegative hybrid factor model

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