title: miRDis: a Web tool for endogenous and exogenous microRNA discovery based on deep-sequencing data analysis.
abstract: Small RNA sequencing is the most widely used tool for microRNA (miRNA) discovery, and shows great potential for the efficient study of miRNA cross-species transport, i.e., by detecting the presence of exogenous miRNA sequences in the host species. Because of the increased appreciation of dietary miRNAs and their far-reaching implication in human health, research interests are currently growing with regard to exogenous miRNAs bioavailability, mechanisms of cross-species transport and miRNA function in cellular biological processes. In this article, we present microRNA Discovery (miRDis), a new small RNA sequencing data analysis pipeline for both endogenous and exogenous miRNA detection. Specifically, we developed and deployed a Web service that supports the annotation and expression profiling data of known host miRNAs and the detection of novel miRNAs, other noncoding RNAs, and the exogenous miRNAs from dietary species. As a proof-of-concept, we analyzed a set of human plasma sequencing data from a milk-feeding study where 225 human miRNAs were detected in the plasma samples and 44 show elevated expression after milk intake. By examining the bovine-specific sequences, data indicate that three bovine miRNAs (bta-miR-378, -181* and -150) are present in human plasma possibly because of the dietary uptake. Further evaluation based on different sets of public data demonstrates that miRDis outperforms other state-of-the-art tools in both detection and quantification of miRNA from either animal or plant sources. The miRDis Web server is available at: http://sbbi.unl.edu/miRDis/index.php.
authors.affiliation: Systems Biology and Biomedical Informatics (SBBI) Laboratory, Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
authors.forename: Hanyuan
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Systems Biology and Biomedical Informatics (SBBI) Laboratory, Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
authors.forename: Bruno
authors.initials: B
authors.lastname: Vieira Resende E Silva
authors.affiliation: Systems Biology and Biomedical Informatics (SBBI) Laboratory, Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
authors.forename: Juan
authors.initials: J
authors.lastname: Cui
mesh_terms: D019295:Computational Biology / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D020407:Internet; D035683:MicroRNAs / Q000032:analysis* / Q000235:genetics*; D058977:Molecular Sequence Annotation; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D035683:MicroRNAs