miRNA-seq / Up-down analysis of miRNA targets


Given a data set of miRNA expression and a data set with gene expression from matching two-group comparison experiments, this tool identifies which of the target genes that behaves oppositely to the expression of the corresponding miRNA.



This tool integrates miRNA and gene expression data from two-group comparison experiments, and identifies which of the target genes behave oppositely to any given miRNA. By default, the tool assumes that the "group" column of the phenodata table is used to define which samples belong to a certain experiment groups, but if another column was used the corresponding parameter should be set up accordingly.

The analysis consists of two parts:

Firstly, predicted target genes for the list of miRNA:s are fetched from the TargetScan and PicTar databases, and only those genes are included which are predicted in both databases. Then, another intersection is made with the list of genes present in the matching gene expression data set.

Secondly, the average expression, either using the mean or median, is calculated for the two experiment groups for each data set and the fold difference calculated. For each up-regulated miRNA the corresponding target genes that are down-regulated are then identified, and a result table listing the miRNA:s, target genes and the fold difference for each is output. Conversely, down-regulated miRNA:s and their up-regulated gene targets are output in a separate result table. Since there is no statistical analysis performed, and hence no confidence measures are reported, it is advisable that the input data has been judiciously filtered and/or subjected to statistical analysis for differential expression prior to invoking this tool.


The output consists of two text files, one listing the up-regulated miRNA:s and their down-regulated gene targets, and the other one listing the down-regulated miRNA:s and their up-regulated gene targets.


This tool leverages some of the functionality from the RmiR Bioconductor package. More info on the databases of predicted miRNA targets can be found at: