PDbase: A database of Parkinson’s Disease-related

genes and genetic variation using substantia nigra ESTs

Jin Ok YangKorean BioInformation Center (KOBIC)

E-mail: joy@kribb.re.kr

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 PDLewy 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 processUniGene collection processUniGene collection processUniGene collection process

Human Cell & TissueHuman Cell & Tissue

cDNA library(Normalized, Full-length)

cDNA library(Normalized, Full-length)

Picking & GriddingPicking & Gridding

Automatic DNA Extraction

Automatic DNA Extraction

Workstation for Sequencing Reaction

Workstation for Sequencing Reaction

PCRPCR

Purification ofReaction Mixture

Purification ofReaction Mixture

Run on Auto-SequencerRun on Auto-Sequencer

Data Editing & AssemblyData Editing & Assembly

UniGene & Fl-lengthcDNA Database

UniGene & Fl-lengthcDNA DatabasecDNA ChipcDNA Chip

cDNA ChipcDNA ChipProteinProtein

ProteinProtein

SourceLibrary Name

Library Type

ReadsUniGene #217*

Gene Clusters

SN normal tissue

Substantia Nigra B6NSN0 Full-length 2,056 600 619

B6NSN0n1 Full-length, Normalized

983 356 375

PD’ SN tissue

Substantia Nigra B7PSN0 Full-length 2,053 738 750

B7PSN0n1 Full-length, Normalized

975 798 831

SN cDNA Libraries Summary

*Number of clusters and genes in NCBI UniGene build#217 contributed by our EST sequences

Alternative Splicing events

AS events Number of Genes associated with AS event

Alternative starts 119

Alternative ends 61

Retained intron 64

Cassette exon 45

Double cassette exon

9

Alternative 3’ exon 32

Alternative 5’ exon 19

We discovered SN ESTs from Full-length cDNA libraries based

on oligo-capping methods

Significant differences in gene expression

PDbase system

PDbaseMerged 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

DiseaseGene & Protein

dbSNPPD-related

SNPs

Web interface

1

2

# GeneSymbol

Description More 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

FTL

*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 http://bioportal.kobic.re.kr/PDbase/