MIRIA: a webserver for statistical, visual and meta-analysis of RNA editing data in mammals

Xikang Feng,Zishuai Wang,Shuai Cheng Li,Hechen Li

doi:10.1186/s12859-019-3242-2

Abstract

BackgroundAdenosine-to-inosine RNA editing can markedly diversify the transcriptome, leading to a variety of critical molecular and biological processes in mammals. Over the past several years, researchers have developed several new pipelines and software packages to identify RNA editing sites with a focus on downstream statistical analysis and functional interpretation.ResultsHere, we developed a user-friendly public webserver named MIRIA that integrates statistics and visualization techniques to facilitate the comprehensive analysis of RNA editing sites data identified by the pipelines and software packages. MIRIA is unique in that provides several analytical functions, including RNA editing type statistics, genomic feature annotations, editing level statistics, genome-wide distribution of RNA editing sites, tissue-specific analysis and conservation analysis. We collected high-throughput RNA sequencing (RNA-seq) data from eight tissues across seven species as the experimental data for MIRIA and constructed an example result page.ConclusionMIRIA provides both visualization and analysis of mammal RNA editing data for experimental biologists who are interested in revealing the functions of RNA editing sites. MIRIA is freely available at https://mammal.deepomics.org.

Highlights

Adenosine-to-inosine RNA editing can markedly diversify the transcriptome, leading to a variety of critical molecular and biological processes in mammals
The most common form of RNA editing, A-to-I RNA editing, is catalysed by the ADAR family of enzymes (Adenosine Deaminase that Acts on RNA) [1, 2], and this process leads to an A-to-G reading of the cDNA molecule [3, 4]
We developed MIRIA (Mammalian RNA Editing Profiling and Interactive Analysis), a webserver which focuses on providing mammalian RNA editing statistics, genomic feature annotations, editing level calculations, Feng et al BMC Bioinformatics 2019, 20(Suppl 24):596 genome-wide distributions of RNA editing sites, tissuespecific analyses and conservation analyses

Summary

Results

To evaluate the MIRIA webserver, we collected 55 RNA-seq datasets from seven mammals (i.e., human, mouse, rat, rhesus, pig, cow, sheep) as the test data. Seven or eight tissue samples (i.e., brain, liver, lung, kidney, spleen, testis, heart, muscle) were used. The RNA-seq data were downloaded from the National Center for Biotechnology Information (NCBI).

Background

Conclusion

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