Protocol to identify regulatory modules in Parkinson’s disease progression using miRNA data and Boolean modeling
Summary: 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, b...
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| Format: | Article |
| Language: | English |
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Elsevier
2025-06-01
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| Series: | STAR Protocols |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166725001753 |
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| author | Ahmed Abdelmonem Hemedan Venkata Satagopam Reinhard Schneider Marek Ostaszewski |
| author_facet | Ahmed Abdelmonem Hemedan Venkata Satagopam Reinhard Schneider Marek Ostaszewski |
| author_sort | Ahmed Abdelmonem Hemedan |
| collection | DOAJ |
| description | Summary: 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 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| format | Article |
| id | doaj-art-599ffdebd1234075b008fd8f32df2d6e |
| institution | OA Journals |
| issn | 2666-1667 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj-art-599ffdebd1234075b008fd8f32df2d6e2025-08-20T01:49:07ZengElsevierSTAR Protocols2666-16672025-06-016210376910.1016/j.xpro.2025.103769Protocol to identify regulatory modules in Parkinson’s disease progression using miRNA data and Boolean modelingAhmed Abdelmonem Hemedan0Venkata Satagopam1Reinhard Schneider2Marek Ostaszewski3Bioinformatics Core Unit, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4367 Esch-sur-Alzette, Luxembourg; Corresponding authorBioinformatics Core Unit, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4367 Esch-sur-Alzette, LuxembourgBioinformatics Core Unit, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4367 Esch-sur-Alzette, LuxembourgBioinformatics Core Unit, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4367 Esch-sur-Alzette, Luxembourg; Corresponding authorSummary: 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 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.http://www.sciencedirect.com/science/article/pii/S2666166725001753BioinformaticsMolecular BiologyNeuroscienceSystems biology |
| spellingShingle | Ahmed Abdelmonem Hemedan Venkata Satagopam Reinhard Schneider Marek Ostaszewski Protocol to identify regulatory modules in Parkinson’s disease progression using miRNA data and Boolean modeling STAR Protocols Bioinformatics Molecular Biology Neuroscience Systems biology |
| title | Protocol to identify regulatory modules in Parkinson’s disease progression using miRNA data and Boolean modeling |
| title_full | Protocol to identify regulatory modules in Parkinson’s disease progression using miRNA data and Boolean modeling |
| title_fullStr | Protocol to identify regulatory modules in Parkinson’s disease progression using miRNA data and Boolean modeling |
| title_full_unstemmed | Protocol to identify regulatory modules in Parkinson’s disease progression using miRNA data and Boolean modeling |
| title_short | Protocol to identify regulatory modules in Parkinson’s disease progression using miRNA data and Boolean modeling |
| title_sort | protocol to identify regulatory modules in parkinson s disease progression using mirna data and boolean modeling |
| topic | Bioinformatics Molecular Biology Neuroscience Systems biology |
| url | http://www.sciencedirect.com/science/article/pii/S2666166725001753 |
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