# Protocol to identify regulatory modules in Parkinson’s disease progression using miRNA data and Boolean modeling

## TL;DR

This paper introduces a protocol to identify regulatory modules in Parkinson’s disease using miRNA data and Boolean modeling to understand disease progression.

## Contribution

A novel protocol for identifying miRNA-driven regulatory modules in Parkinson’s disease using Boolean modeling and cohort-specific data.

## Key findings

- The protocol outlines steps for omics data collection and Boolean model construction to identify PD regulatory modules.
- Modules identified explain how miRNA mechanisms influence Parkinson’s disease progression in specific cohorts.
- Model validation procedures ensure the reliability of results using experimental PD data.

## Abstract

Regulatory modules are molecules that interact functionally, driving disease processes. Here, we present a protocol for identifying regulatory modules in Parkinson’s disease (PD) using cohort-specific microRNA (miRNA) data and Boolean modeling. We describe steps for omics data collection, biomolecule and miRNA target analysis, and Boolean model construction and simulation. We then detail procedures for validation of the model and results. The modules identified using this protocol explain how miRNA-driven mechanisms influence PD progression in disease cohorts.

For complete details on the use and execution of this protocol, please refer to Hemedan et al.1

•Steps for identifying cohort-specific PD modules via Boolean modeling•Instructions for miRNA target enrichment in PD pathways•Procedures for simulating molecular shifts in PD cohorts•Guidance on model validation with experimental PD data

Steps for identifying cohort-specific PD modules via Boolean modeling

Instructions for miRNA target enrichment in PD pathways

Procedures for simulating molecular shifts in PD cohorts

Guidance on model validation with experimental PD data

Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Regulatory modules are molecules that interact functionally, driving disease processes. Here, we present a protocol for identifying regulatory modules in Parkinson’s disease (PD) using cohort-specific microRNA (miRNA) data and Boolean modeling. We describe steps for omics data collection, biomolecule and miRNA target analysis, and Boolean model construction and simulation. We then detail procedures for validation of the model and results. The modules identified using this protocol explain how miRNA-driven mechanisms influence PD progression in disease cohorts.