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

Ahmed Abdelmonem Hemedan; Venkata Satagopam; Reinhard Schneider; Marek Ostaszewski

doi:10.1016/j.xpro.2025.103769

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

Ahmed Abdelmonem Hemedan^*
, Venkata Satagopam
, Reinhard Schneider
, Marek Ostaszewski^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Research › peer-review

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

Original language	English
Article number	103769
Journal	STAR Protocols
Volume	6
Issue number	2
DOIs	https://doi.org/10.1016/j.xpro.2025.103769
Publication status	Published - 20 Jun 2025
Externally published	Yes

Keywords

Bioinformatics
Molecular Biology
Neuroscience
Systems biology
MicroRNAs/genetics
Humans
Computational Biology/methods
Gene Regulatory Networks
Disease Progression
Parkinson Disease/genetics

Access to Document

10.1016/j.xpro.2025.103769

Cite this

@article{1816fa042d5e4acb9e28b4cd37eaf046,

title = "Protocol to identify regulatory modules in Parkinson's disease progression using miRNA data and Boolean modeling",

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",

keywords = "Bioinformatics, Molecular Biology, Neuroscience, Systems biology, MicroRNAs/genetics, Humans, Computational Biology/methods, Gene Regulatory Networks, Disease Progression, Parkinson Disease/genetics",

author = "Hemedan, \{Ahmed Abdelmonem\} and Venkata Satagopam and Reinhard Schneider and Marek Ostaszewski",

year = "2025",

month = jun,

day = "20",

doi = "10.1016/j.xpro.2025.103769",

language = "English",

volume = "6",

journal = "STAR Protocols",

issn = "2666-1667",

publisher = "Cell Press",

number = "2",

}

TY - JOUR

T1 - Protocol to identify regulatory modules in Parkinson's disease progression using miRNA data and Boolean modeling

AU - Hemedan, Ahmed Abdelmonem

AU - Satagopam, Venkata

AU - Schneider, Reinhard

AU - Ostaszewski, Marek

PY - 2025/6/20

Y1 - 2025/6/20

N2 - 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

AB - 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

KW - Bioinformatics

KW - Molecular Biology

KW - Neuroscience

KW - Systems biology

KW - MicroRNAs/genetics

KW - Humans

KW - Computational Biology/methods

KW - Gene Regulatory Networks

KW - Disease Progression

KW - Parkinson Disease/genetics

UR - https://www.scopus.com/pages/publications/105004426312

U2 - 10.1016/j.xpro.2025.103769

DO - 10.1016/j.xpro.2025.103769

M3 - Article

C2 - 40347476

AN - SCOPUS:105004426312

SN - 2666-1667

VL - 6

JO - STAR Protocols

JF - STAR Protocols

IS - 2

M1 - 103769

ER -

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

Abstract

Keywords

Access to Document

Other files and links

Fingerprint

Cite this