# MiDNE a tool for Multi-omics genes and drugs interactions discovery

## TL;DR

MiDNE is a new tool that combines multi-omics data and drug information to discover gene and drug interactions in cancer, helping to identify potential therapeutic strategies.

## Contribution

MiDNE introduces a novel computational framework for integrating multi-omics and pharmacological data to uncover disease-specific gene-drug interactions.

## Key findings

- MiDNE integrates gene expression, methylation, proteomic, and copy number variation data with drug-target interactions.
- The tool was benchmarked on Breast Invasive Carcinoma and Glioblastoma multiforme, revealing actionable gene-drug relationships.
- MiDNE provides a user-friendly Shiny web application for easy exploration of multi-omics and drug interaction data.

## Abstract

The availability of models representing molecular interactions in complex pathologies is essential for understanding their molecular setup and identifying therapeutic vulnerabilities. In this context, the advent of high-throughput technologies has enabled the rapid and cost-effective profiling of multiple omics layers, driving a paradigm shift from generalized models to disease-specific, context-aware modeling approaches. While the analysis of individual omics layers can provide information about specific aspects of cellular biology for a given disease, it often fails to capture complex interactions among molecules and drugs operating across different regulatory levels. Here, we introduce MiDNE (Multi-omics genes and Drugs Network Embedding), a novel computational framework that integrates experimental multi-omics data with pharmacological knowledge to uncover disease specific multi-omics gene and drug interactions. MiDNE integrates omics-specific networks, derived from experimental data, with known drug interactors in a multiplex heterogeneous network. It applies a network embedding procedure based on the random walk with restart algorithm to project genes and drugs into a shared multi-omics latent space, enabling gene–drug clustering and neighborhood search. We demonstrate the potential of MiDNE on Breast Invasive Carcinoma and Glioblastoma multiforme, by integrating gene expression, methylation, proteomic, and copy number variation profiles with curated drug–target interactions. By providing multilayer and disease-specific views of gene and drug interactions, MiDNE facilitates the discovery of actionable gene–drug relationships and the development of precision pharmacological strategies. MiDNE is available as both an open-source R package and a Shiny web application.

•MiDNE is a novel R package for integrating gene-centered multi-omics and drug data.•MiDNE allows the discovery of gene–gene, drug–gene, and drug–drug associations from cancer derived omics data.•MiDNE offers a user-friendly Shiny interface enables easy execution and exploration of its pipeline.•MiDNE has been benchmarked using BRCA and GBM multi-omics data and FDA-approved drugs.•MiDNE provides a network-based tool for cancer research and drug repurposing.

MiDNE is a novel R package for integrating gene-centered multi-omics and drug data.

MiDNE allows the discovery of gene–gene, drug–gene, and drug–drug associations from cancer derived omics data.

MiDNE offers a user-friendly Shiny interface enables easy execution and exploration of its pipeline.

MiDNE has been benchmarked using BRCA and GBM multi-omics data and FDA-approved drugs.

MiDNE provides a network-based tool for cancer research and drug repurposing.