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Genome Biology & Applied Bioinformatics SNPs Mehmet Tevfik DORAK, MD PhD

Genome Biology & Applied Bioinformatics SNPs Mehmet Tevfik DORAK, MD PhD. Schedule. Outline. Individual SNP Analysis ( SNiPA , rVARbase ) Multiple SNP Analysis ( PheGenI , SNPnexus ) eQTL Resources Browsers Functionality Scores for the Whole Genome.

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Genome Biology & Applied Bioinformatics SNPs Mehmet Tevfik DORAK, MD PhD

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  1. Genome Biology & Applied Bioinformatics SNPs Mehmet Tevfik DORAK, MD PhD

  2. Schedule

  3. Outline Individual SNP Analysis (SNiPA, rVARbase) Multiple SNP Analysis (PheGenI, SNPnexus) eQTL Resources Browsers Functionality Scores for the Whole Genome

  4. Interpretation of GWAS Findings: Individual SNPs

  5. Interpretation of GWAS Findings: Individual SNPs

  6. Interpretation of GWAS Findings: Multiple SNPs

  7. Interpretation of GWAS Findings: Multiple SNPs

  8. Interpretation of GWAS Findings: Multiple SNPs

  9. eQTL Resources: GTEx Results from multiple tissues from the same persons

  10. eQTLResources: GTEx

  11. eQTLResources: GTEx

  12. eQTLResources: GTEx Address: http://www.gtexportal.org/home/bubbleHeatmapPage/ACTN3

  13. eQTLResources: GTEx Address: http://www.gtexportal.org/home/gene/RASSF2

  14. eQTL Resources

  15. eQTL Resources

  16. eQTL and meQTL Expression Quantitative Trait Locus: eQTL Methylation Quantitative Trait Locus: meQTL (most relevant in complex diseases) * * * * Non-synonymous (missense) or non-sense mutations directly affect protein structure or translation (more relevant in Mendelian than complex diseases)

  17. BIOS QTL Browser for eQTL/meQTL analysis Assesses both eQTL and meQTL status of a SNP

  18. mQTLdb for meQTL analysis Results from five life stages

  19. Browsers

  20. Functionality Scores for the Whole Genome CADD scores: http://cadd.gs.washington.edu/download DANN scores: https://cbcl.ics.uci.edu/public_data/DANN/data EIGEN scores: http://www.columbia.edu/~ii2135/download.html RegulomeDB scores: http://regulomedb.org/downloads dbWGFP Scores: http://bioinfo.au.tsinghua.edu.cn/dbwgfp/downloads.php?page=downlite Pre-computed Structure-PPi scores for COSMIC and 1KG mutations: http://structureppi.bioinfo.cnio.es/Structure

  21. Functionality Scores for the Whole Genome 22 different annotations corresponding to either conservation score or biochemical activity, including 2 genomic conservation measures, 2 indicators of open chromatin, 8 histone modifications, and 10 TFBS peaks.

  22. Functionality Scores for the Whole Genome 22 different annotations corresponding to either conservation score or biochemical activity, including 2 genomic conservation measures, 2 indicators of open chromatin, 8 histone modifications, and 10 TFBS peaks.

  23. … Looking forward …..

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