Quantitative prediction of NF-kappa B DNA-protein interactions.

ABSTRACT: We describe a general method based on principal coordinates analysis to predict the effects of single-nucleotide polymorphisms within regulatory sequences on DNA-protein interactions. We use binding data for the transcription factor NF-kappaB as a test system. The method incorporates the effects of interactions between base pair positions in the binding site, and we demonstrate that such interactions are present for NF-kappaB. Prediction accuracy is higher than with profile models, confirmed by crossvalidation and by the experimental verification of our predictions for additional sequences. The binding affinities of all potential NF-kappaB sites on human chromosome 22, together with the effects of known single-nucleotide polymorphisms, are calculated to determine likely functional variants

SUBMITTER: Udalova IA 

PROVIDER: S-EPMC123039 | biostudies-literature | 2002 Jun

REPOSITORIES: biostudies-literature