Computational regulatory network construction from microRNA and transcription factor perspectives

Authors:
Sungmin Rhee;Jinwoo Park;Sun Kim
Affiliations:
Seoul National University, Seoul, Korea;Seoul National University, Seoul, Korea;Seoul National University, Seoul, Korea
Venue:
ACM SIGBioinformatics Record
Year:
2013

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Abstract

As more genomic and epigenomic data becomes available, it has become possible to construct biological networks from the omics data. Among the biological networks, understanding gene regulatory mechanisms is a very important research problem that can reveal condition-specific, e.g., disease-specific, gene regulatory mechanisms. In this paper, we review the current development in the study of constructing gene regulatory networks from microRNA and transcription factor (TF) perspectives. TFs and microRNAs play crucial role in gene regulatory networks since they regulate tens to hundreds of genes, which can be seen naturally as hubs in the network. This review consists of three parts. The first part summarizes recent works on TF regulatory network reconstruction in two sections, one on TF network reconstruction using time series gene expression data and the other on TF network construction by incorporating prior knowledge. The second part is about microRNA network construction in two sections, one on methods based on seed sequence matching and the other on the integrated analysis of gene and microRNA expression data sets. The last part summarizes recent works on the integration of both TF and microRNA with target genes, which is a much more challenging research problem.