Email updates

Keep up to date with the latest news and content from BMC Bioinformatics and BioMed Central.

Open Access Highly Accessed Research article

Finding quasi-modules of human and viral miRNAs: a case study of human cytomegalovirus (HCMV)

Isana Veksler-Lublinsky1, Yonat Shemer-Avni2, Eti Meiri3, Zvi Bentwich2, Klara Kedem1 and Michal Ziv-Ukelson1*

Author Affiliations

1 Department of Computer Science, Ben-Gurion University, Beer-Sheva 84105, Israel

2 Virology and Developmental Genetics/Health Sciences, Ben-Gurion University

3 , Rosetta Genomics Ltd., 10 Plaut St., Rehovot, 76706, Israel

For all author emails, please log on.

BMC Bioinformatics 2012, 13:322  doi:10.1186/1471-2105-13-322

Published: 3 December 2012

Abstract

Background

MicroRNAs (miRNAs) are important regulators of gene expression encoded by a variety of organisms, including viruses. Although the function of most of the viral miRNAs is currently unknown, there is evidence that both viral and host miRNAs contribute to the interactions between viruses and their hosts. miRNAs constitute a complex combinatorial network, where one miRNA may target many genes and one gene may be targeted by multiple miRNAs. In particular, viral and host miRNAs may also have mutual target genes. Based on published evidence linking viral and host miRNAs there are three modes of mutual regulation: competing, cooperating, and compensating modes.

Results

In this paper we explore the compensating mode of mutual regulation upon Human Cytomegalovirus (HCMV) infection, when host miRNAs are down regulated and viral miRNAs compensate by mimicking their function. To achieve this, we develop a new algorithm which finds groups, called quasi-modules, of viral and host miRNAs and their mutual target genes, and use a new host miRNA expression data for HCMV-infected and uninfected cells. For two of the reported quasi-modules, supporting evidence from biological and medical literature is provided.

Conclusions

The modules found by our method may advance the understanding of the role of miRNAs in host-viral interactions, and the genes in these modules may serve as candidates for further experimental validation.