ArticleBMC genomics2009
PDbase: a database of Parkinson's disease-related genes and genetic variation using substantia nigra ESTs.
Article in BMC genomics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 27 citations in OpenAlex.
- The Alpha-Synuclein Gene (SNCA) is a Genomic Target of Methyl-CpG Binding Protein 2 (MeCP2)-Implications for Parkinson's Disease and Rett Syndrome.Molecular neurobiology · 2024Article
- NDDRF: A risk factor knowledgebase for personalized prevention of neurodegenerative diseases.Journal of advanced research · 2022Article
- Gene4PD: A Comprehensive Genetic Database of Parkinson's Disease.Frontiers in neuroscience · 2021Article
- Translational Informatics for Parkinson's Disease: from Big Biomedical Data to Small Actionable Alterations.Genomics, proteomics & bioinformatics · 2019Review
- Network and Pathway-Based Analyses of Genes Associated with Parkinson's Disease.Molecular neurobiology · 2017Article
- NeuroDNet - an open source platform for constructing and analyzing neurodegenerative disease networks.BMC neuroscience · 2013Article
- Emerging roles of epigenetic mechanisms in Parkinson's disease.Functional & integrative genomics · 2011Review
- Human protein reference database and human proteinpedia as discovery resources for molecular biotechnology.Molecular biotechnology · 2011Article
- Extending Asia Pacific bioinformatics into new realms in the "-omics" era.BMC genomics · 2009Article
Corrections and comments
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundParkinson's disease (PD) is one of the most common neurodegenerative disorders, clinically characterized by impaired motor function. Since the etiology of PD is diverse and complex, many researchers have created PD-related research resources. However, resources for brain and PD studies are still lacking. Therefore, we have constructed a database of PD-related gene and genetic variations using the substantia nigra (SN) in PD and normal tissues. In addition, we integrated PD-related information from several resources.
resultsWe collected the 6,130 SN expressed sequenced tags (ESTs) from brain SN normal tissues and PD patients SN tissues using full-cDNA library and normalized cDNA library construction methods from our previous study. The SN ESTs were clustered in 2,951 unigene clusters and assigned in 2,678 genes. We then found up-regulated 57 genes and down-regulated 48 genes by comparing normal and PD SN ESTs frequencies with over 0.9 cut-off probability of differential expression based on the Audic and Claverie method. In addition, we integrated disease-related information from public resources. To examine the characteristics of these PD-related genes, we analyzed alternative splicing events, single nucleotide polymorphism (SNP) markers located in the gene regions, repeat elements, gene regulation elements, and pathways and protein-protein interaction networks.
conclusionWe constructed the PDbase database to capture the PD-related gene, genetic variation, and functional elements. This database contains 2,698 PD-related genes through ESTs discovered from human normal and PD patients SN tissues, and through integrating several public resources. PDbase provides the mitochondrion proteins, microRNA gene regulation elements, single nucleotide polymorphisms (SNPs) markers within PD-related gene structures, repeat elements, and pathways and networks with protein-protein interaction information. The PDbase information can aid in understanding the causation of PD. It is available at http://bioportal.kobic.re.kr/PDbase/. Supplementary data is available at http://bioportal.kobic.re.kr/PDbase/suppl.jsp.
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