isomiRex: Web‐based identification of microRNAs, isomiR variations and differential expression using next‐generation sequencing datasets

Abstract

Edited by Paul BertoneKeywords: isomiRs MicroRNA Next generation sequencing Web platform a b s t r a c tWe present an open-access web platform isomiRex, to identify isomiRs and on the fly graphical visualization of the differentially expressed miRNAs in control as well as treated library. The open-access web-platform is not restricted only to NGS sequence dataset from animals and potentially analyzes a wider dataset for plants, animals and viral NGS dataset supporting miRBase (version 19 supporting 193 species). The platform can handle the bloated amount of the read counts and reports the annotated microRNAs from plant, animal and viral NGS datasets. isomiRex also provides an estimation of the the isomiRs, of miRNAs with higher copy number relative to their mature reference sequences indexed in miRBase (version 19 supporting 193 species). Visually enhanced graphs potentially display differentially expressed isomiRs, which will help the user to demonstrate and correlate the abundance of the isomiR as a signature event to the specific condition. An additional module for estimating the differential expression has been implemented allowing the users to postulate the differential expression across the user input samples. The developed web-platform can be accessed at

Virus versus Host Plant MicroRNAs: Who Determines the Outcome of the Interaction?

“…The observed differences in isomiR expression could be influenced by recognition of the target site or/and binding capacity by the AGO complex [73], [91]. However, miRNA length variation could also reflect various downstream effects and might have important functional implications [91], [93], which were demonstrated in Arabidopsis thaliana with different activities on AGO1 and for individual loci in Prunus persica [93]–[95].…”

Emerging techniques to decipher microRNAs (miRNAs) and their regulatory role in conferring abiotic stress tolerance of plants

“…High-throughput characterization and classification of isomiRs in plants can be obtained via isomiRex (http:// bioinfo1.uni-plovdiv.bg/isomiRex/) (Sablok et al 2013). de Oliveira et al (2013) and Muller et al (2014), respectively, introduced isomiRID (http://www.ufrgs.br/RNAi/isomiRID/ ) and isomiRage (http://cru.genomics.iit.it/Isomirage) which uses template-and non-template-based predictions to differentiate between isomiRs.…”

sRNAbench: profiling of small RNAs and its sequence variants in single or multi-species high-throughput experiments

“…Open Access [10], miRDeep [11], miRanalyzer [12], SeqBuster [13], NiBLS [14], miRTRAP [15], MIReNA [16], miRanalyzer [17], DARIO [18], UEA sRNA workbench [19], segmentSeq [20], CPSS [21], ncPRO-seq [22], miRDeep2 [23], ShortStack [24], isomiRex [25], mirDeep* [26], mirTools 2.0 [27] among others. These tools detect and profile small RNAs either by mapping the sequencing reads first to the genome (using a genome annotation on a second step) or by direct mapping to reference sequence libraries in FASTA format.…”