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Prediction of transcription factor binding to DNA using rule induction methods

Huss, Mikael ; Nordström, Karin

Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516)

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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 domain 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 TF-DNA 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 the primary motivation for introducing the rule induction based methods is the lack of efficient algorithms for paired domain-DNA binding prediction, we also show that the method can be applied with some success to a more well-studied TF-DNA binding prediction task involving the early growth response (EGR) TF family.

Institution: Faculty of Technology, Research Groups in Informatics
DDC classification: Data processing, computer science, computer systems

Suggested Citation:
Huss, Mikael ; Nordström, Karin  (2006)  Prediction of transcription factor binding to DNA using rule induction methods. Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516), 3(2), 2006. Special Issue: 3rd Integrative Bioinformatics Workshop, Harpenden, United Kingdom, 2

Online-Journal: http://journal.imbio.de/index.php?paper_id=42
URL: http://biecoll.ub.uni-bielefeld.de/volltexte/2007/223

Also published by Shaker:
Ralf Hofestädt, Thoralf Töpel (eds.). Integrative Bioinformatics -
Yearbook 2006. Shaker, 2007.

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