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SNP@Promoter : A database of Human SNPs (Single Nucleotide Polymorphisms) within putative promoter region

SNP@Promoter : A database of Human SNPs (Single Nucleotide Polymorphisms) within putative promoter region. Korea BioInformation Center Byoung-Chul Kim. Korean Bioinformation Center (KOBIC). The national bioinformatics center of Korea

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SNP@Promoter : A database of Human SNPs (Single Nucleotide Polymorphisms) within putative promoter region

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  1. SNP@Promoter: 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)

  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 ( http://biowiki.net )

  4. Toolbar Drag the module from the list and drop it into the design view. Ontology View Design View Monitoring View BioPipe • 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. http://www.biopipe.net

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

  6. Common DNA sequence variations among individualsin 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 What are SNPs (Single Nucleotide Polymorphisms)

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

  8. KOBIC Variome Project Http://variome.net

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

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

  11. Predicted TFBS Ontology Conservation of TFBS Annotation SNP within TFBS Pathway SNP within Promoter Disease association What can you do with SNP@Promoter? SNP Gene GAD GOA OMIM UCSC Transfac NCBI dbSNP KEGG 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. SNP@promoter is a database Predict functional SNPs Provide a platform for biologists for finding functional SNPs http://variome.kobic.re.kr http://variome.kobic.re.kr/SNPatPromoter/ Conclusions

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