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

Differential expression analysis (DEA) is one of the main instruments utilized for revealing molecular mechanisms in pathological and physiological conditions. DIANA-mirExTra v2.0 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).

Interactive network graph output from mirExTra v2.0 functional analysis module


The network depicts up- and down-regulated TFs (green and red, respectively) along with their miRNA targets (blue and pink). The module was set to identify TFs functioning as activators and therefore targets and regulators tend to be correspondingly differentially expressed. Each regulator node (green/red nodes) hosts the regulator name, while target nodes (blue/pink nodes) depict the number of grouped targets. By selecting a target node all grouped targets are presented in the relevant pane (bottom right).

Availability – DIANA-mirExTra v2.0 has an intuitive user interface and is freely available to all users without any login requirement. http://www.microrna.gr/mirextrav2

Vlachos IS, Vergoulis T, Paraskevopoulou MD, Lykokanellos F, Georgakilas G, Georgiou P, Chatzopoulos S, Karagkouni D, Christodoulou F, Dalamagas T, Hatzigeorgiou AG. (2016) DIANA-mirExTra v2.0: Uncovering microRNAs and transcription factors with crucial roles in NGS expression data. Nucleic Acids Res [Epub ahead of print]. [article]

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