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

Similar protocols

Protocol publication

[…] Two in silico programs were used. FASTSNP is a web-based tool for assessing phenotypic effects of SNPs through the use of external web servers and a prediction algorithm. FASTSNP uses a ranking system from 0 (no known effect) to 5 (very high risk) based on location of the SNP (eg, 5′ upstream, 3′ untranslated region, intronic) and possible functional effects such as amino acid changes, alterations in splicing sites, and “premature translation termination”.F-SNP also utilizes bioinformatic tools and websites to predict the functional effects of SNPs. The process has several steps, with each step determining the next. For instance, if a mutation is found in the coding region through Ensembl, the information is then submitted to an outside bioinformatics website, such as PolyPhen, to test for functional effect. […]

Pipeline specifications

Software tools FastSNP, PolyPhen
Databases F-SNP
Application GWAS
Diseases Neoplasms