Integration of gene expression, genome wide DNA methylation, and gene networks for clinical outcome prediction in ovarian cancer

Lin Zhang, Hui Liu, Jia Meng, Xuesong Wang, Yidong Chen, Yufei Huangi

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Integrative clinical outcome prediction model called gene interaction regularized elastic net (GIREN) method is proposed in this paper. GIREN combines gene expression, methylation profiles, and gene interaction networks in order to reveal genomic and epigenomic features that bear important prognostic value. With GIREN, gene expression and DNA methylation profiles are first jointly analyzed in a linear regression model, and additional gene interaction network is simultaneously integrated as a regularizing penalty that follow an elastic net formulation. Such regularization also enforce sparsity in the solution so that features with prognostic values are automatically selected. To solve the regularized optimization, an iterative gradient descent algorithm is also developed. We applied GIREN to a set of 87 human ovarian cancer samples, which underwent a rigorous sample selection. The predicted outcome was used to group patients into high-risk vs. low-risk. Validation showed that GIREN outperformed other competing algorithms including SuperPCA.

Original languageEnglish (US)
Title of host publicationProceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013
Pages535-538
Number of pages4
DOIs
StatePublished - Dec 1 2013
Event2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013 - Shanghai, China
Duration: Dec 18 2013Dec 21 2013

Publication series

NameProceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013

Other

Other2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013
CountryChina
CityShanghai
Period12/18/1312/21/13

ASJC Scopus subject areas

  • Biomedical Engineering

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  • Cite this

    Zhang, L., Liu, H., Meng, J., Wang, X., Chen, Y., & Huangi, Y. (2013). Integration of gene expression, genome wide DNA methylation, and gene networks for clinical outcome prediction in ovarian cancer. In Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013 (pp. 535-538). [6732553] (Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013). https://doi.org/10.1109/BIBM.2013.6732553