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Bhak, Jong
KOrean GenomIcs Center(KOGIC)
Research Interests
  • Geromics, genomics, bioinformatics, protein Engineering, OMICS


PDbase: A database of Parkinson's disease-related genes and genetic variation using substantia nigra ESTs

DC Field Value Language Yang, Jin Ok ko Kim, Woo-Yeon ko Jeong, So-Young ko Oh, Jung-Hwa ko Jho, Sungwoong ko Bhak, Jong Hwa ko Kim, Nam-Soon ko 2015-08-03T00:13:43Z - 2015-07-31 ko 2009-12 -
dc.identifier.citation BMC GENOMICS, v.10, no.SUPPL. 3, pp.S32 - ko
dc.identifier.issn 1471-2164 ko
dc.identifier.uri -
dc.identifier.uri ko
dc.description.abstract Background: Parkinson'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. Results: We 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. Conclusion: We 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 Supplementary data is available at © 2009 Yang et al; licensee BioMed Central Ltd ko
dc.description.statementofresponsibility close -
dc.language ENG ko
dc.publisher BIOMED CENTRAL LTD ko
dc.subject microRNA ko
dc.subject mitochondrial protein ko
dc.subject complementary DNA ko
dc.title PDbase: A database of Parkinson's disease-related genes and genetic variation using substantia nigra ESTs ko
dc.title.alternative PDbase: a database of Parkinson's Disease-related genes and genetic variation using substantia nigra ESTs ko
dc.type ARTICLE ko
dc.identifier.scopusid 2-s2.0-71549167886 ko
dc.type.rims ART ko
dc.description.scopustc 8 * 2015-11-04 *
dc.identifier.doi 10.1186/1471-2164-10-S3-S32 ko
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