PDbase : A database of Parkinson’s Disease-related genes and genetic variation using substantia nigra ESTs Jin Ok Yang Korean BioInformation Center (KOBIC)

Abbreviation PD: Parkinson’s Disease SN: Substantia Nigra

Parkinson’ Disease (PD) PD  Neurodegenerative movement disorder  Late-onset neurological disorder, after the age of 50 Symptoms : slowness of movement, rest tremor, rigidity, anxiety, depression, disturbance in balance, autonomic disturbance Degeneration of dopaminergic (DA) neurons in Substantia Nigra (SN) : loss of pigmented neurons in the pars compacta of the SN

Pathology & Diagnosis of PD  Degeneration of Dopaminergic Neurons in Substantia Nigra  Lewy body : pathologic hallmark of PD, cytoplasmic inclusion body PET scan Normal PD Lewy Body

Background The substantia nigra (SN) is important resource to understand the mechanism of the PD causation The needs for the resources to provide information of comprehensive PD-related genes and genetic variations We present a consolidated PD database, called PDbase, to capture wide spectrum of molecular events

PDbase database PDbase – A comprehensive PD-related genes and genetic variation database – Contains 2,678 genes and 870,468 SNPs from 1) SN ESTs and 2) public disease- related databases – Provides biological function of the PD-related genes including alternative splicing events, SNPs located in gene structure, mitochondrial proteins, micro-RNA elements, biological pathways, and PPI networks Related work MDPD (The Mutation Database for Parkinson’s Disease) – 202 genes extracted from 576 publications and manually examined by biomedical researchers based on population studies – It provides the PD-related genetic variation effects such as risk factor or ethnic group PDGene – 40~80 PD genetic association studies – PD-related genes and risk factors from association studies

PDbase construction: SN EST discovery and computational analysis

** Information of SN samples - normal SN tissue ; male caucasian 81 yrs of age, died congestive heart failure, negative for HIV 1/2, HBV and HCV. - PD’s SN ; male caucasian 60 yrs of age, diagnosed with PD, died from a gun shot wound, negative for HIV 1/2, HBV and HCV. Global approaches  Useful in the analysis of complex biological phenomena, including certain human diseases.  Helpful to examine general gene expression in the transcriptome. Substantia Nigra (SN) ESTs collection

Cell and Tissue Banking Parkinson’s disease : - PD’s SN Tissues - Normal SN Tissues High-diverse cDNA library Full-length cDNA library Normalized cDNA library Large-scale cDNA sequencing Automatic colony picking Automatic plasmid DNA prep Automatic reaction mixing Base call, Editing, and Clustering Phrep & Phred CAP3 Bioinformatics Group UniGene collection process Human Cell & Tissue cDNA library (Normalized, Full-length) cDNA library (Normalized, Full-length) Picking & Gridding Automatic DNA Extraction Automatic DNA Extraction Workstation for Sequencing Reaction Workstation for Sequencing Reaction PCR Purification of Reaction Mixture Purification of Reaction Mixture Run on Auto-Sequencer Data Editing & Assembly UniGene & Fl-length cDNA Database UniGene & Fl-length cDNA Database cDNA Chip ProteinProtein

Source Library Name Library TypeReads UniGene #217* GeneClusters SN normal tissue Substantia NigraB6NSN0Full-length2, B6NSN0n1Full-length, Normalized PD’ SN tissue Substantia NigraB7PSN0Full-length2, B7PSN0n1Full-length, Normalized SN cDNA Libraries Summary *Number of clusters and genes in NCBI UniGene build#217 contributed by our EST sequences

Alternative Splicing events AS eventsNumber of Genes associated with AS event Alternative starts119 Alternative ends61 Retained intron64 Cassette exon45 Double cassette exon9 Alternative 3’ exon32 Alternative 5’ exon19 We discovered SN ESTs from Full- length cDNA libraries based on oligo- capping methods

Significant differences in gene expression

PDbase system

PDbase Merged PD-related Gene information Alternative splicing events (UniGene isoforms) Gene regulation Gene Ontology Biological Pathways Protein-protein Interaction Normal SN ESTs PD’ SN ESTs Homologous genes (BLAST) Differential expression (Audic algorithm) PD-related genes dbSNP PD-related SNPs mitoDat HGNC Refseq Uniprot Mapping (BLAST) HGMD GAD OMIM UMLS Disease Gene & Protein dbSNP PD-related SNPs

Web interface 1 2

#Gene Symbol DescriptionMore Information

Query Results – SN EST statistics – Gene information – Genetic variation information – Gene regulation – Gene Ontology (GO) – Biological pathways: BioCarta and KEGG – Protein-protein interaction network

Results_1 for the selected gene

Results_2 for the selected gene

FT L *Partners  FTH1  MAP3K12  GADD45A  PTN  MYOC  SMAD9  KNG1  TAF10  MPHOSPH6  MPP6  PUNC

Conclusion PDbase – Provides comprehensive information about Parkinson’s Disease-related genes and genetic variation – highlights to contain not only public resources, but also un-reported PD target genes using normal and PD’s SN ESTs – Helpful in analysis of complex biological phenomena including human brain diseases because of including several genes, genetic variations, expression, and network – available at