MEDIAproject

MEDIAproject data pre-processing, Consensus signature extraction and patient-centric approach

These codes are related to the paper “Identification of therapeutic targets in osteoarthritis by combining heterogeneous transcriptional datasets,drug-induced expression profiles, and known drug-target interactions” DOI: https://doi.org/10.1186/s12967-024-05006-z

The pre-processing steps, DE analyses, Consensus signature extraction and patient-centric approach are accessible at the following links:

1. Single-cell Pre-processing and DE analysis;

2. Bulk data Pre-processing and DE analysis;

3. Consensus signature extraction and enrichment;

4. Validation dataset analyses and enrichment;

5. Patient-centric approach;

6. Enrichment analyses: volcanos and bubble plots

MEDIAproject Disease-centric approach

The repository includes an R Markdown file for drug prioritization and a Python notebook for the generation of the network

The repository includes several useful files for reproducibility named “Useful_files.zip” *** Please notice that we identified an error in the bubble charts published in the original paper. Instead of computing the color code as -log10(p.adjust), we inadvertently used the natural logarithm (-log(p.adjust)). This mistake resulted in a slight adjustment to the color range in the plots, but it did not alter the conclusions drawn from the analysis. The error did not affect the final deduction in any meaningful way, as both methods ultimately lead to the same interpretation of the data. We apologize for any confusion caused and have rectified the code in the “6. Enrichment analyses: volcanoes and bubble plots” section.