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.
Dr. Jacopo Ronchi 
Dr. Maria Foti
1School of Medicine and Surgery, University of Milano-Bicocca, Italy
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
| Path | Description |
|---|---|
'Alzheimer's disease'/ |
The R scripts used for pre-processing and analysis of the AD case study. |
'Benchmark on simulated data'/ |
The R scripts and helper functions used to generate synthetic miRNA–mRNA datasets and to evaluate the performance of various correlation-based and categorical methods. |
'Clear cell renal cell carcinoma'/ |
The R scripts used for pre-processing and analysis of the ccRCC dataset. |
'Dilated cardiomyopathy'/ |
The R scripts used for the analysis of the DCM dataset. |
logo.png |
The MIRit logo. |
README.md |
This file. |
LICENSE |
License terms for the code. |
The performance of MIRit has been tested with three different datasets:
- A sample-matched experiment in which miRNA and mRNA expression were evaluated in patients with dilated cardiomyopathy using miRNA-Seq and RNA-Seq, respectively.
- 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.
- 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.
This code is distributed under the GNU General Public License v3.0 (GPLv3).