MIRit Supporting Files

This repository contains the analysis files used in the manuscript to demonstrate the effectiveness of MIRit in integrative miRNA-mRNA analyses. For more information on how MIRit works, please refer to the original paper. The source code of MIRit is accessible on GitHub.

Authors

Dr. Jacopo Ronchi ¹ (author and maintainer)

Dr. Maria Foti ¹

¹School of Medicine and Surgery, University of Milano-Bicocca, Italy

Reference

The publication that details the implementation of MIRit and its usage is currently available on bioRxiv:

Ronchi J and Foti M. ‘MIRit: an integrative R framework for the identification of impaired miRNA-mRNA regulatory networks in complex diseases’. bioRxiv (2023). doi:10.1101/2023.11.24.568528

Datasets description

The performance of MIRit has been tested with three different datasets:

1. A sample-matched experiment in which miRNA and mRNA expression were evaluated in patients with dilated cardiomyopathy using miRNA-Seq and RNA-Seq, respectively.
2. A sample-matched experiment in which miRNA and mRNA expression were profiled in clear cell renal cell carcinoma (ccRCC) samples and normal adjacent renal tissue.
3. A dataset without matched samples, in which miRNA expression was evaluated in postmortem BA9 tissue from a cohort of patients with Alzheimer's disease (AD) and gene expression was assessed using microarray technology in the same brain region, but in a different cohort of patients.

The datasets used in this study are publicly available on GEO under the accession numbers GSE243406, GSE16441, GSE63501, and GSE150696.

File organization

The R scripts used to generate the results presented in the manuscript can be found in the "Dilated Cardiomyopathy," "Clear Cell Renal Cell Carcinoma," and "Alzheimer's Disease" folders. R scripts used for data preprocessing are also included when necessary.