Volume 5 Number 3 (May 2015)
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IJBBB 2015 Vol.5(3): 175-183 ISSN: 2010-3638
doi: 10.17706/ijbbb.2015.5.3.175-183

Large Causal Gene Regulatory Network Inference by Decomposition into Subnetworks

Leung-Yau Lo, Man-Leung Wong, Kin-Hong Lee, Kwong-Sak Leung
Abstract—Inferring the gene regulatory network is an important first step toward understanding the working of the cell and consequently curing diseases related to malfunctioning of the cell. One thorny problem in gene regulatory network inference is that even with high throughput technology, the available time series expression data is still very limited compared to the network size. To alleviate this problem, we propose to decompose large network into small subnetworks without prior knowledge of the decomposition. Our algorithm first infers an initial GRN using CLINDE, then decomposes it into possibly overlapping subnetworks, then infers each subnetwork by either CLINDE or DD-lasso and finally merges the subnetworks. We have tested this algorithm on synthetic data of networks with 500 and 1000 genes. Results show that our proposed algorithm does improve the GRN inference performance of using either CLINDE or DD-lasso alone on the large network, with statistical significance, and is robust to different variances and slight deviation from Gaussian distribution in error terms.

Index Terms—Decomposition, large gene network inference, time delay, time series expression data.

Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong.
Department of Computing and Decision Sciences, Lingnan University, Tuen Mun, Hong Kong.

Cite: Leung-Yau Lo, Man-Leung Wong, Kin-Hong Lee, Kwong-Sak Leung, "Large Causal Gene Regulatory Network Inference by Decomposition into Subnetworks," International Journal of Bioscience, Biochemistry and Bioinformatics vol. 5, no. 3, pp. 175-183, 2015.

General Information

ISSN: 2010-3638 (Online)
Abbreviated Title: Int. J. Biosci. Biochem. Bioinform.
Frequency: Quarterly 
DOI: 10.17706/IJBBB
Editor-in-Chief: Prof. Ebtisam Heikal 
Abstracting/ Indexing:  Electronic Journals Library, Chemical Abstracts Services (CAS), Engineering & Technology Digital Library, Google Scholar, and ProQuest.
E-mail: ijbbb@iap.org
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