Functional in Silico Analysis of Gene Regulatory Polymorphism

Abstract

Regulatory polymorphisms play important roles in determining phenotypes and disease susceptibilities through perturbing gene expression. After genetic markers with LD have been mapped, an important task is to evaluate their functional importance based on the identification of regulatory regions and specific regulatory elements. Here we introduce the leading bioinformatics tools and invaluable resources to facilitate the functional analysis in silico. We focus on promoter prediction, modeling, prediction of transcription factor binding sites and identification of sequence elements important for splicing regulation. These tools are becoming increasingly accurate and powerful to guide experimental investigations and to transform correlated alleles into mechanistic understandings.

Prioritizing Disease Genes and Understanding Disease Pathways

“…De-novo motif finding methods have been developed to discover novel enriched motifs in a set of sequences. We refer to (Zhang, Zhao, & Zhang, 2007) for details on the topic of motif finding. A recent study used TF binding sites similarity to prioritize disease genes (Aerts et al, 2006).…”

Identificação de genes de suscetibilidade herdada para o melanoma cutâneo por genotipagem em larga escala

“…Aproximadamente 1% deles estavam em regiões que codificam proteínas. Esses números foram considerados adequados, uma vez que foi observado em estudos prévios que regiões regulatórias da expressão gênica são altamente polimórficas (Zhang et al, 2007).…”