Next-Generation Sequencing of Small RNAs from HIV-Infected Cells Identifies Phased microRNA Expression Patterns and Candidate Novel microRNAs Differentially Expressed upon Infection

Chang, Stewart T.; Thomas, Matthew J.; Sova, Pavel; Green, Richard R.; Palermo, Robert E.; Katze, Michael G.

To identify the possible biological effects of DE microRNAs in HIV-infected cells, we examined the annotations (pathways and functions) associated with their predicted, anticorrelated target mRNAs. Specifically, we compared the number of target mRNAs to the number of DE mRNAs associated with each annotation term and determined those annotations with a significant overrepresentation of target mRNAs. We assumed that annotations with an abundance of target mRNAs were more likely to identify pathways regulated by microRNAs. We also examined the set of microRNA-mRNA interactions associated with each annotation to identify possible hub (highly connected) microRNAs and mRNAs. Hub microRNAs may be important regulators of multiple mRNAs, while hub mRNAs may be robustly regulated by multiple microRNAs.