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http://bura.brunel.ac.uk/handle/2438/18213
Title: | Integration of Multi-omics Data for Gene Regulatory Network Inference and Application to Breast Cancer |
Authors: | Yuan, L Guo, LH Yuan, CA Zhang, YH Han, K Nandi, A Honig, B Huang, DS |
Keywords: | biweight midcorrelation,;differential correlation,;nonconvex penalty,;gene regulatory network,;stability selection |
Issue Date: | 23-Aug-2018 |
Publisher: | Institute of Electrical and Electronics Engineers |
Citation: | IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2018 |
Abstract: | Underlying a cancer phenotype is a specific gene regulatory network that represents the complex regulatory relationships between genes. However, it remains a challenge to find cancer-related gene regulatory network because of insufficient sample sizes and complex regulatory mechanisms in which gene is influenced by not only other genes but also other biological factors. With the development of high-throughput technologies and the unprecedented wealth of multi-omics data give us a new opportunity to design machine learning method to investigate underlying gene regulatory network. In this paper, we propose an approach, which use biweight midcorrelation to measure the correlation between factors and make use of nonconvex penalty based sparse regression for gene regulatory network inference (BMNPGRN). BMNCGRN incorporates multi-omics data (including DNA methylation and copy number variation) and their interactions in gene regulatory network model. The experimental results on synthetic datasets show that BMNPGRN outperforms popular and state-of-the-art methods (including DCGRN, ARACNE and CLR) under false positive control. Furthermore, we applied BMNPGRN on breast cancer (BRCA) data from The Cancer Genome Atlas database and provided gene regulatory network. |
URI: | http://bura.brunel.ac.uk/handle/2438/18213 |
DOI: | http://dx.doi.org/10.1109/TCBB.2018.2866836 |
ISSN: | 1545-5963 http://dx.doi.org/10.1109/TCBB.2018.2866836 |
Appears in Collections: | Dept of Electronic and Electrical Engineering Research Papers |
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