Genome Biology Applied Bioinformatics SNPs Mehmet Tevfik DORAK
Genome Biology & Applied Bioinformatics SNPs Mehmet Tevfik DORAK, MD Ph. D YOUR FUTURE STARTS WITH HOPE
Schedule
Outline Individual SNP Analysis (SNi. PA, r. VARbase) Multiple SNP Analysis (Phe. Gen. I, SNPnexus) e. QTL Resources Browsers Functionality Scores for the Whole Genome
Interpretation of GWAS Findings: Individual SNPs
Interpretation of GWAS Findings: Individual SNPs
Interpretation of GWAS Findings: Multiple SNPs
Interpretation of GWAS Findings: Multiple SNPs
Interpretation of GWAS Findings: Multiple SNPs
e. QTL Resources: GTEx Results from multiple tissues from the same persons
e. QTL Resources: GTEx
e. QTL Resources: GTEx
e. QTL Resources: GTEx Address: http: //www. gtexportal. org/home/bubble. Heatmap. Page/ACTN 3
e. QTL Resources: GTEx Address: http: //www. gtexportal. org/home/gene/RASSF 2
e. QTL Resources
e. QTL Resources
e. QTL and me. QTL Expression Quantitative Trait Locus: e. QTL Methylation Quantitative Trait Locus: me. QTL (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)
BIOS QTL Browser for e. QTL/me. QTL analysis Assesses both e. QTL and me. QTL status of a SNP
m. QTLdb for me. QTL analysis Results from five life stages
Browsers
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/~ii 2135/download. html Regulome. DB scores: http: //regulomedb. org/downloads db. WGFP Scores: http: //bioinfo. au. tsinghua. edu. cn/dbwgfp/downloads. php? page=downlite Pre-computed Structure-PPi scores for COSMIC and 1 KG mutations: http: //structureppi. bioinfo. cnio. es/Structure
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.
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.
… Looking forward …. . YOUR FUTURE STARTS WITH HOPE
YOUR FUTURE STARTS WITH HOPE
- Slides: 25