DIANA-mirExTra v2.0: Uncovering microRNAs and transcription factors with crucial roles in NGS expression data

Abstract

Differential expression analysis (DEA) is one of the main instruments utilized for revealing molecular mechanisms in pathological and physiological conditions. DIANA-mirExTra v2.0 (http://www.microrna.gr/mirextrav2) performs a combined DEA of mRNAs and microRNAs (miRNAs) to uncover miRNAs and transcription factors (TFs) playing important regulatory roles between two investigated states. The web server uses as input miRNA/RNA-Seq read count data sets that can be uploaded for analysis. Users can combine their data with 350 small-RNA-Seq and 65 RNA-Seq in-house analyzed libraries which are provided by DIANA-mirExTra v2.0.The web server utilizes miRNA:mRNA, TF:mRNA and TF:miRNA interactions derived from extensive experimental data sets. More than 450 000 miRNA interactions and 2 000 000 TF binding sites from specific or high-throughput techniques have been incorporated, while accurate miRNA TSS annotation is obtained from microTSS experimental/in silico framework. These comprehensive data sets enable users to perform analyses based solely on experimentally supported information and to uncover central regulators within sequencing data: miRNAs controlling mRNAs and TFs regulating mRNA or miRNA expression. The server also supports predicted miRNA:gene interactions from DIANA-microT-CDS for 4 species (human, mouse, nematode and fruit fly). DIANA-mirExTra v2.0 has an intuitive user interface and is freely available to all users without any login requirement.

microCLIP super learning framework uncovers functional transcriptome-wide miRNA interactions

“…AGO-PAR-CLIP datasets from nine studies, corresponding to 13 cell lines in human species, were derived from GEO 7 , 39 and DDBJ 40 repositories (Supplementary Table 1 ). Fifteen small RNA-Seq and 9 RNA-Seq experiments of similar cell types with PAR-CLIP libraries were analyzed following methodologies as described by Vlachos et al 41 to infer expressed miRNAs and transcripts. (s)RNA-Seq datasets were derived from the ENCODE repository and from a series of studies (Supplementary Tables 10 , 11 ).…”

Examining the Genetic Background of Porcine Muscle Growth and Development Based on Transcriptome and miRNAome Data

“…Moreover, the analysis of miRNA–target gene interactions was performed with the use of the DIANA-mirExTra v2.0 [ 10 ] (DIANA-Lab, Athens, Greece) tool to identify functional microRNAs potentially responsible for changes in gene expression identified in the present study as DEGs. mRNA and microRNA differential expression analysis results were simultaneously analysed, and important miRNA regulators were identified based on functional analysis of their target genes.…”

Manatee: detection and quantification of small non-coding RNAs from next-generation sequencing data

“…www.nature.com/scientificreports www.nature.com/scientificreports/ Methods Multimap analysis. Quality-check and pre-processing of all libraries utilized in multimaps analysis was performed as in Vlachos et al 28 . In brief, dataset quality control was performed using FastQC 29 .…”