Integration of multiple genomic imaging data for the study of schizophrenia using joint nonnegative matrix factorization

Min Wang; Ting Zhu Huang; Vince D. Calhoun; Jian Fang; Yu Ping Wang

doi:10.1109/ICASSP.2017.7952323

Integration of multiple genomic imaging data for the study of schizophrenia using joint nonnegative matrix factorization

Min Wang, Ting Zhu Huang, Vince D. Calhoun, Jian Fang, Yu Ping Wang

School of Medicine

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

1 Scopus citations

Abstract

Schizophrenia (SZ) is a complex disease caused by a lot genetic variants, epigenetic and brain region abnormalities. In this study, we adopted a joint nonnegative matrix factorization method to integrate three datasets including single nucleotide polymorphism (SNP), brain activity measured by functional magnetic resonance imaging (fMRI) and DNA Methylation to identify multi-dimensional modules associated with SZ. They are then used to study the coordination between regulatory mechanisms at multiple levels. This method projects multiple types of data onto a common feature space, in which heterogeneous variables with large coefficients on the same projected bases form a multi-dimensional module. The genomic factors in such modules have significant correlations and likely functional associations with brain activities. We applied this method to the real data analysis and identified multi-dimensional modules including SNP, fMRI and DNA methylation sites. These selected biomarkers were finally used to identify genes and voxels, which were confirmed to be significantly associated with SZ.

Original language	English (US)
Title of host publication	2017 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2017 - Proceedings
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	1083-1087
Number of pages	5
ISBN (Electronic)	9781509041176
DOIs	https://doi.org/10.1109/ICASSP.2017.7952323
State	Published - Jun 16 2017
Event	2017 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2017 - New Orleans, United States Duration: Mar 5 2017 → Mar 9 2017

Publication series

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

Other

Other	2017 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2017
Country/Territory	United States
City	New Orleans
Period	3/5/17 → 3/9/17

Keywords

Feature selection
Joint nonnegative matrix factorization
Methylation
SNP
fMRI

ASJC Scopus subject areas

Software
Signal Processing
Electrical and Electronic Engineering

Access to Document

10.1109/ICASSP.2017.7952323

Cite this

Wang, M., Huang, T. Z., Calhoun, V. D., Fang, J., & Wang, Y. P. (2017). Integration of multiple genomic imaging data for the study of schizophrenia using joint nonnegative matrix factorization. In 2017 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2017 - Proceedings (pp. 1083-1087). Article 7952323 (ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/ICASSP.2017.7952323

Integration of multiple genomic imaging data for the study of schizophrenia using joint nonnegative matrix factorization. / Wang, Min; Huang, Ting Zhu; Calhoun, Vince D. et al.
2017 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2017 - Proceedings. Institute of Electrical and Electronics Engineers Inc., 2017. p. 1083-1087 7952323 (ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings).

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

Wang, M, Huang, TZ, Calhoun, VD, Fang, J & Wang, YP 2017, Integration of multiple genomic imaging data for the study of schizophrenia using joint nonnegative matrix factorization. in 2017 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2017 - Proceedings., 7952323, ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings, Institute of Electrical and Electronics Engineers Inc., pp. 1083-1087, 2017 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2017, New Orleans, United States, 3/5/17. https://doi.org/10.1109/ICASSP.2017.7952323

Wang M, Huang TZ, Calhoun VD, Fang J, Wang YP. Integration of multiple genomic imaging data for the study of schizophrenia using joint nonnegative matrix factorization. In 2017 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2017 - Proceedings. Institute of Electrical and Electronics Engineers Inc. 2017. p. 1083-1087. 7952323. (ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings). doi: 10.1109/ICASSP.2017.7952323

Wang, Min ; Huang, Ting Zhu ; Calhoun, Vince D. et al. / Integration of multiple genomic imaging data for the study of schizophrenia using joint nonnegative matrix factorization. 2017 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2017 - Proceedings. Institute of Electrical and Electronics Engineers Inc., 2017. pp. 1083-1087 (ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings).

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Integration of multiple genomic imaging data for the study of schizophrenia using joint nonnegative matrix factorization

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