Prediction of transcription factor binding to DNA using rule induction methods

In this study, we seek to develop a predictive model for finding the strength of binding between a particular transcription factor (TF) variant and a particular DNA target variant. The DNA binding paired domains of the Pax transcription factors, which are our main focus, show seemingly fuzzy and degenerate binding to various DNA targets, and paired domain-DNA binding is not a problem well suited for previously proposed algorithms. Here, we introduce a simple way to use rule induction for predicting the strength of TFDNA binding. We have created a dataset consisting of 597 example cases for paired domain-DNA binding by collecting information about all published and quantified interactions between TF and DNA sequence variants. Application of the rule induction based method on this dataset yields a high, although far from ideal accuracy of 69.7% (based on cross-validation), but perhaps more importantly, several useful rules for predicting the binding strength have been found. Although th...

• Type: Journal
• Year: 2006
• Where: JIB
• Authors: Mikael Huss, Karin Nordström
• Keywords: Dna Targets, JIB 2006, Rule Induction, Transcription Factor