Inference of gene regulatory subnetworks from time course gene expression data

BMC Bioinformatics
Xi-Jun LiangFang-Xiang Wu

Abstract

Identifying gene regulatory network (GRN) from time course gene expression data has attracted more and more attentions. Due to the computational complexity, most approaches for GRN reconstruction are limited on a small number of genes and low connectivity of the underlying networks. These approaches can only identify a single network for a given set of genes. However, for a large-scale gene network, there might exist multiple potential sub-networks, in which genes are only functionally related to others in the sub-networks. We propose the network and community identification (NCI) method for identifying multiple subnetworks from gene expression data by incorporating community structure information into GRN inference. The proposed algorithm iteratively solves two optimization problems, and can promisingly be applied to large-scale GRNs. Furthermore, we present the efficient Block PCA method for searching communities in GRNs. The NCI method is effective in identifying multiple subnetworks in a large-scale GRN. With the splitting algorithm, the Block PCA method shows a promosing attempt for exploring communities in a large-scale GRN.

References

Jun 13, 2002·Proceedings of the National Academy of Sciences of the United States of America·M Girvan, M E J Newman
Feb 26, 2004·Proceedings of the National Academy of Sciences of the United States of America·Filippo RadicchiDomenico Parisi
Mar 11, 2009·IEEE Transactions on Information Technology in Biomedicine : a Publication of the IEEE Engineering in Medicine and Biology Society·Xiaohua HuBahrad A Sokhansanj
Feb 19, 2010·Biometrics·Mihee LeeJ S Marron
Nov 26, 2010·Conference Proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society·Fang-Xiang WuZhang-Hang Xia

Citations

Related Concepts

Gene Expression
Computational Molecular Biology
Gene Modules
Gene Expression
Genes
Neural Networks (Anatomic)
Hodgkin's Granuloma, Unspecified Site, Extranodal and Solid Organ Sites
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Structure
Grn protein, mouse

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