title: PDbase: a database of Parkinson's disease-related genes and genetic variation using substantia nigra ESTs.
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.
  
  
  CONCLUSIONS
  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 http://bioportal.kobic.re.kr/PDbase/. Supplementary data is available at http://bioportal.kobic.re.kr/PDbase/suppl.jsp.
authors: Korean Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), 111 Gwahangno, Yuseong-gu, Daejeon 305-806, Korea. joy@kribb.re.kr
authors: Jin Ok
authors: JO
authors: Yang
authors: Woo-Yeon
authors: WY
authors: Kim
authors: So-Young
authors: SY
authors: Jeong
authors: Jung-Hwa
authors: JH
authors: Oh
authors: Sungwoong
authors: S
authors: Jho
authors: Jong
authors: J
authors: Bhak
authors: Nam-Soon
authors: NS
authors: Kim
mesh_terms: D018076:DNA, Complementary / Q000737:chemistry / Q000235:genetics; D030561:Databases, Nucleic Acid; D015536:Down-Regulation; D020224:Expressed Sequence Tags; D015723:Gene Library; D014644:Genetic Variation; D006801:Humans; D020407:Internet; D010300:Parkinson Disease / Q000235:genetics*; D013378:Substantia Nigra / Q000737:chemistry*; D015854:Up-Regulation
chemical_list: D018076:DNA, Complementary