miRDis: A Web tool for endogenous and exogenous microRNA discovery based on deep-sequencing data analysis

Hanyuan Zhang, Bruno Vieira Resende e Silva, Juan Cui

Research output: Contribution to journalArticle

4 Citations (Scopus)

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 proofof- 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.

Original languageEnglish (US)
Pages (from-to)415-424
Number of pages10
JournalBriefings in bioinformatics
Volume19
Issue number3
DOIs
StatePublished - May 1 2018

Fingerprint

High-Throughput Nucleotide Sequencing
RNA
MicroRNAs
Plasma (human)
Web services
Animals
Servers
Pipelines
Health
Plasmas
RNA Sequence Analysis
Milk
Biological Phenomena
Untranslated RNA

Keywords

  • Endogenous microRNA
  • Exogenous microRNA
  • MicroRNA expression
  • Novel microRNA
  • microRNA sequencing

ASJC Scopus subject areas

  • Information Systems
  • Molecular Biology

Cite this

miRDis : A Web tool for endogenous and exogenous microRNA discovery based on deep-sequencing data analysis. / Zhang, Hanyuan; e Silva, Bruno Vieira Resende; Cui, Juan.

In: Briefings in bioinformatics, Vol. 19, No. 3, 01.05.2018, p. 415-424.

Research output: Contribution to journalArticle

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