title: Finding quasi-modules of human and viral miRNAs: a case study of human cytomegalovirus (HCMV).
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.
authors.affiliation: Department of Computer Science, Ben-Gurion University, Beer-Sheva 84105, Israel.
authors.forename: Isana
authors.initials: I
authors.lastname: Veksler-Lublinsky
authors.forename: Yonat
authors.initials: Y
authors.lastname: Shemer-Avni
authors.forename: Eti
authors.initials: E
authors.lastname: Meiri
authors.forename: Zvi
authors.initials: Z
authors.lastname: Bentwich
authors.forename: Klara
authors.initials: K
authors.lastname: Kedem
authors.forename: Michal
authors.initials: M
authors.lastname: Ziv-Ukelson
mesh_terms: D000465:Algorithms; D003587:Cytomegalovirus / Q000235:genetics* / Q000502:physiology; D015536:Down-Regulation; D005786:Gene Expression Regulation / Q000502:physiology*; D006801:Humans; D035683:MicroRNAs / Q000502:physiology*; D012367:RNA, Viral / Q000502:physiology*
chemical_list: D035683:MicroRNAs; D012367:RNA, Viral