PDmethDB: A curated Parkinson's disease associated methylation information database.
Changliang Wang1,2, Liang Chen3,4, Menglei Zhang1
1Cancer Centre, Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Macau S.A.R., China.
Computational and Structural Biotechnology Journal
|December 11, 2020
Summary
Parkinson's disease (PD) is linked to DNA hypomethylation, where α-synuclein affects DNA Methyltransferase 1 (DNMT1). PDmethDB is a new database curating methylation data to aid research into PD's epigenetic underpinnings.
Area of Science:
- Neuroscience
- Epigenetics
- Bioinformatics
Background:
- Parkinson's disease (PD) is the second leading neurodegenerative disorder, characterized by Lewy bodies primarily composed of α-synuclein.
- α-Synuclein sequesters DNA Methyltransferase 1 (DNMT1), a key DNA methylation enzyme, from the nucleus to the cytoplasm, causing global DNA hypomethylation in the human brain.
- DNA methylation is a crucial epigenetic mechanism regulating gene expression, yet specific databases for PD-associated methylation data are lacking.
Purpose of the Study:
- To establish PDmethDB, a comprehensive database curating Parkinson's disease-associated methylation information from scientific literature.
- To facilitate research on the intricate relationship between epigenetic modifications, specifically DNA methylation, and the pathogenesis of Parkinson's disease.
- To provide a centralized, searchable resource for researchers studying PD and its molecular underpinnings.
Main Methods:
- Systematic literature review of approximately 1600 published papers to extract relevant methylation data.
- Curation of data including gene/molecule name, CpG site, methylation and expression alterations, tissue, publication ID (PMID), and experimental methods.
- Development of a user-friendly web interface for searching, browsing, downloading, and submitting data, including gene interaction network visualization.
Main Results:
- PDmethDB currently houses 97,077 entries related to PD methylation, covering 12,308 molecules, 37,944 CpG sites, 31 tissues, and 3 species.
- The database provides detailed information on methylation and expression alterations, experimental methodologies, and tissue-specific data.
- Includes interactive features like gene interaction networks, highlighting PD-associated genes from DisGeNET.
Conclusions:
- PDmethDB serves as a valuable, centralized resource for researchers investigating the role of DNA methylation in Parkinson's disease.
- The database aims to advance the understanding of epigenetic dysregulation in PD by consolidating and presenting extensive methylation-related information.
- Facilitates exploration of molecular mechanisms and potential therapeutic targets through accessible data and network analysis.
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