MIRit Supporting Files

This repository contains the analysis files that were used in the paper to showcase the performance of MIRit for integrative miRNA-mRNA analyses. For details regarding the functioning of MIRit, please refer to the original publication. The source code of the R package is available on GitHub in the main repository of MIRit.

Authors

Dr. Jacopo Ronchi ¹ (author and maintainer)

Dr. Maria Foti ¹

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

Reference

The corresponding publication where we describe the implementation of MIRit and its usage is 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

MIRit's behavior has been tested with two different datasets:

• sequencing data obtained from Riesco-Eizaguirre et al. (2015) who profiled gene and miRNA expression in 8 papillary thyroid carcinoma tumors and corresponding contralateral tissue from the same patients;
• a small RNA-Seq experiment that examines post-mortem BA9 tissues from 6 patients with AD and 7 healthy controls, in addition to transcriptomic data where the BA9 region has been profiled in 9 patients with AD and 9 healthy donors through microarray technology.

All the datasets are obtained from Gene Expression Omnibus (GEO), with accession numbers: GSE63511, GSE63501, and GSE150696. Before the analyses, data preprocessing was carried out as described in the manuscript. Only preprocessed expression data are included in this repository, whereas raw data are available on GEO.

File organization

The analysis files for each example are stored in the relative folders: "Thyroid cancer" and "Alzheimer's disease". Specifically, each example contains:

• The R script that was used to generate the results, thyroid_cancer_analysis.R for the first example and alzheimer_analysis.R for the second one,
• A data folder with processed expression matrices and sample metadata,
• A results folder containing the raw results of the analysis;
• A plots folder that stores the generated figures used in the manuscript.