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. 2013 Jul;10(7):1087-92.
doi: 10.4161/rna.25193. Epub 2013 May 29.

mirTools 2.0 for non-coding RNA discovery, profiling, and functional annotation based on high-throughput sequencing

Jinyu Wu  1 , Qi Liu, Xin Wang, Jiayong Zheng, Tao Wang, Mingcong You, Zhong Sheng Sun, Qinghua Shi
Affiliations

mirTools 2.0 for non-coding RNA discovery, profiling, and functional annotation based on high-throughput sequencing

Jinyu Wu et al. RNA Biol. 2013 Jul.

Abstract

Next-generation sequencing has been widely applied to understand the complexity of non-coding RNAs (ncRNAs) in a cost-effective way. In this study, we developed mirTools 2.0, an updated version of mirTools 1.0, which includes the following new features. (1) From miRNA discovery in mirTools 1.0, mirTools 2.0 allows users to detect and profile various types of ncRNAs, such as miRNA, tRNA, snRNA, snoRNA, rRNA, and piRNA. (2) From miRNA profiling in mirTools 1.0, mirTools 2.0 allows users to identify miRNA-targeted genes and performs detailed functional annotation of miRNA targets, including Gene Ontology, KEGG pathway and protein-protein interaction. (3) From comparison of two samples for differentially expressed miRNAs in mirTools 1.0, mirTools 2.0 allows users to detect differentially expressed ncRNAs between two experimental groups or among multiple samples. (4) Other significant improvements include strategies used to detect novel miRNAs and piRNAs, more taxonomy categories to discover more known miRNAs and a stand-alone version of mirTools 2.0. In conclusion, we believe that mirTools 2.0 (122.228.158.106/mr2_dev and centre.bioinformatics.zj.cn/mr2_dev) will provide researchers with more detailed insight into small RNA transcriptomes.

Keywords: miRNA; miRNA targets; mirTools; ncRNA; next-generation sequencing; web server.

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Figures

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Figure 1. Output screenshots of mirTools 2.0. The output includes: (1) basic statistics, such as length distribution, percentage of reads aligned to the reference genome, chromosome distribution, functional categories of reads and ncRNA distribution; (2) known miRNA, putative novel miRNA, miRNA isoforms and modification; (3) miRNA-targeted genes and functional annotation based on GO, the KEGG pathway and the PPI network; (4) expression information of other types of ncRNA, such as rRNA, tRNA, snRNA, snoRNA and piRNA; and (5) differentially expressed ncRNAs between two cases, two experimental groups or among multiple samples.
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Figure 2. The overall workflow of mirTools 2.0. The workflow includes clean and filtering raw reads, alignment of them to the reference genome, classification of aligned reads, detection of expression levels of various types of ncRNAs and the differentially expressed ncRNAs between two cases/two experiment groups or among multiple samples, prediction of novel miRNAs and piRNAs, identification of miRNA targeted genes and further functional annotation based on GO, the KEGG pathway and the PPI network.
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