https://www.youtube.com/watch?v=xmXhunLbitU /mnt/1T-5e7/mycodehtml/Biology/SangSooKim/Bioinformatics_basic/004/002_SNP_dbSNP/main.html ================================================================================ SNP: CG is replaced with TA ================================================================================ If one SNP is discovered in many people: it's polymorphic (common variant) ================================================================================ - A is converted into G - But codon designates "Ala" - G is converted into A - And it produces different protein ================================================================================ Pharmaco-genetics ================================================================================ - This is general case - People in general case have much enzymes for digesting drug - Bad effect of drug can be reduced - Only small amount of drug affects body ================================================================================ Inspect all SNPs which human being has and create dbSNP dbSNP: SNP database ================================================================================ - How to create refSNP common_refSNP=common(SNP_from_labortory1,SNP_from_labortory2,SNP_from_labortory3) - rs104894764 is SNP in XIAP gene ================================================================================ /home/young/Pictures/2019_07_01_07:45:35.png - rs104894764 single nucleotide variation SNP ================================================================================ - 2 strands - This part can be called G or C based on strand ================================================================================ - This database speaks data based on upper strand (Fwd strand) ================================================================================ - In RefSNP DB, it's G or T in forward strands - In other words, many people have G but there is some people who have T ================================================================================ - "Ancestral Allele:G" means common ancester of human being has G - How to know it? If mammalian animals have G in common, researchers can say human ancester would also have G ================================================================================ - Variant (such as G is converted into T) can cause disease ================================================================================ This is important information ================================================================================ - NP: protein - NC: chromosome - 1-22 - 23: sexual chromosome X - 24: sexual chromosome Y - In X chromosome - 123,019,864 th base pair - "originally G" is converted into T as SNP ================================================================================ - 11 version (newer version than 10 version) - Contents itself is same but the coordination of SNP base pair is different - 123,886,014 th base pair (800000 base pairs are added from the version 10) - "originally G" is converted into T ================================================================================ - NM: messenger RNA - c: coding - 352th base pair in mRNA's coding region - 118th amino acid in protein - "originally Glu amino acid" is replaced with "Ter (terminating)" codon - Why there are 2 mRNA? Due to alternative splicing ================================================================================ ================================================================================ - Version information ================================================================================ - annotation is contained in XIAP gene ================================================================================ - Changed base - Changed protein ================================================================================ 4 SNPs ================================================================================ - You are seeing this now