PDbase:
A database of Parkinson’s Disease-related genes
and genetic variation using substantia nigra
ESTs
Jin Ok Yang
Korean 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
Normal
PET scan
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 diseaserelated 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
Substantia Nigra (SN) ESTs collection
• Global approaches
 Useful in the analysis of complex biological
phenomena, including certain human diseases.
 Helpful to examine general gene expression
in the transcriptome.
** 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.
UniGene collection process
• Cell and Tissue Banking
Human Cell & Tissue
Parkinson’s disease :
- PD’s SN Tissues
- Normal SN Tissues
cDNA library
(Normalized, Full-length)
Picking & Gridding
• High-diverse cDNA library
Automatic
DNA Extraction
Full-length cDNA library
Normalized cDNA library
Workstation for
Sequencing Reaction
• Large-scale cDNA sequencing
PCR
Automatic colony picking
Automatic plasmid DNA prep
Automatic reaction mixing
Purification of
Reaction Mixture
Run on Auto-Sequencer
• Base call, Editing, and Clustering
Phrep & Phred
CAP3
Bioinformatics Group
Data Editing & Assembly
cDNA Chip
UniGene & Fl-length
cDNA Database
Protein
SN cDNA Libraries Summary
Source
Library
Name
Library Type
Reads
B6NSN0
Full-length
B6NSN0n1
UniGene #217*
Gene
Clusters
2,056
600
619
Full-length,
Normalized
983
356
375
B7PSN0
Full-length
2,053
738
750
B7PSN0n1
Full-length,
Normalized
975
798
831
SN normal tissue
Substantia Nigra
PD’ SN tissue
Substantia Nigra
*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 Fulllength cDNA libraries
based on oligocapping methods
Significant differences in gene expression
PDbase system
Homologous
genes
PD’ SN ESTs
Normal SN
ESTs
(BLAST)
Differential
expression
(Audic
algorithm)
Alternative
splicing events
(UniGene
isoforms)
PD-related SNPs
dbSNP
Gene regulation
Gene Ontology
Merged PD-related
Gene information
PDbase
Biological Pathways
Protein-protein
Interaction
PD-related genes
PD-related SNPs
Gene & Protein
Disease
Refseq
UMLS
Uniprot
Mapping
(BLAST)
HGNC
mitoDat
dbSNP
HGMD
GAD
OMIM
Web interface
1
2
#
Gene
Symbol
Description
More
Information
Query Results
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–
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–
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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
*Partners
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FTL
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/