1. Korea BioInformation Center Byoung-Chul Kim
: A database of Human SNPs (Single Nucleotide Polymorphisms) within putative promoter region
Korea BioInformation Center
Byoung-Chul Kim

2. Korean Bioinformation Center (KOBIC)
The national bioinformatics center of Korea
Mission is to integrate of diverse biological information
Genome information
Biodiversity information
Bioresource information
Work towards the development of international training programs on bioinformatics
Develop bioinformatics tools and resources which need your participation
BioWiki (online knowledgebase of biology)
BioPipe (Bioworkflow engine) 2

3. BioWiki
Wiki
a web technology that enables anyone to create and update website contents.
well suited for developing online knowledge bases (e.g., Wikipedia ).
BioWiki
Project that in order to adopt the wiki paradigm in biology
Goal is the collaborative development of biological knowledge bases.
BioWiki Contest ( ) 3

4. BioPipe To participate in, please visit. http://www.biopipe.net
Design View
Ontology View
Monitoring View
Toolbar
Drag the module from the list and drop it into the design view.
BioWorkFlow Engine
Design of bioinformatics pipelines
No installation required
Drag, Drop and Connect
Biopipe Contest
- openfree Web 2.0
- period : Aug 15th ~ Sep 20th
To participate in, please visit. 4

5. Korea BioInformation Center Byoung-Chul Kim
: A database of Human SNPs (Single Nucleotide Polymorphisms) within putative promoter region
Korea BioInformation Center
Byoung-Chul Kim

6. What are SNPs (Single Nucleotide Polymorphisms)
Common DNA sequence variations among individuals in genome wherein the least frequent allele has an abundance of 1% or greater.
Make up about 90% of all human genetic variation
Occurs every 100 to 300 bases along the 3-billion-bases human genome
Some SNPs are reported to be highly related to diseases or influence cells response to a drug

7. SNPs have various functions
G/T
promoter
G/T
G/C GU AG
TFBS
5’UTR
atggacgtactggtg
tctgagtgctccgcg
3’UTR
A/G
G/T
Type 1 transcript
Type 2 transcript
Type 3 transcript
Type 1 protein
M D V L V S E C S A
Altering the encoded protein
Alternative splicing
Premature termination
Transcription regulation
M D V L V S E S S A
Type 2 protein
Type 3 protein

8. KOBIC Variome Project

9. SNP@Promoter is constructed such as…
Identification of
putative promoter
regions
NCBI Entez
Genes
NCBI Human
Genome
Transfac
Prediction of
Transcription
factor binding sites
NCBI dbSNP
SNPs within
regulatory region
UCSC human
conservation score
Calculation of
Evolution
conservation
score in TFBS
KEGG
HGMD
OMIM
GAD
GOA
Integration of
Functional
annotation
databases

10. We can improve the predictive sensitivity of TFBS
Prediction of TFBS have high false-positive rate
Evolutionarily conserved regions within or adjoining the gene often serve as critical cis-regulatory regions
show the predicted TFBS with evolutionary conservation score
UCSC GENOME BROWSER

11. What can you do with SNP@Promoter?
Gene
Predicted
TFBS
Ontology
Conservation of
TFBS
Pathway
Annotation
SNP
within Promoter
SNP
within
TFBS
GAD
GOA
OMIM
UCSC
Disease
association
KEGG
NCBI
dbSNP
Transfac
HGMD
Human
Genome
NCBI
Gene

12. Example : Atopy associated genes and SNPs

13. Atopy associated gene list

14. SNPs in atopy associated gene

15. Graphic viewer

16. Conclusions http://variome.kobic.re.kr
is a database
Predict functional SNPs
Provide a platform for biologists for finding functional SNPs