Lack of correlation between in silico projection of function and quantitative real-time PCR-determined gene expression levels in colon tissue.

ABSTRACT: There are a number of in silico programs that use algorithms and external web sources to predict the effect of single nucleotide polymorphisms (SNPs). While many of these programs have been shown to predict accurately the effect of SNPs in functional areas of the gene, such as 5' upstream or coding regions, empiric research may be warranted to confirm the functional consequences of SNPs that are predicted to have little to no effect. We compared predictions from FASTSNP (Function Analysis and Selection Tool for Single Nucleotide Polymorphism) and F-SNP (Functional Single Nucleotide Polymorphism) with experimentally derived genotype-phenotype correlations to determine the accuracy of these programs in predicting SNP functionality. We used normal colon tissue to evaluate 24 TagSNPs within si

SUBMITTER: Penney RB 

PROVIDER: S-EPMC3791675 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature