On the Effects of Transcription Factor Properties on the Information Content of Binding Sit.pdf


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^}[_)$\Ac On the Effects of Transcription Factor Properties on the Information Content of Binding Sites Jan T. Kim, Thomas Martinetz, Daniel Polani Institut für Neuro- und Bioinformatik Seelandstraße 1a, 23569 Lübeck, Germany phone: +49 451 3909-585, fax: +49 451 3909-545 email: {kim,martinetz,polani}@informatik.mu-luebeck.de 1 Introduction Networks of genes which encode transcription factors (regulatory networks) play a central role in the realization of phenotypic traits based on genetic information. Sequence-specific recogni- tion of DNA subsequences by proteins is a key mechanism in constituting regulatory networks. Understanding the information theoretic principles underlying the evolution of transcription factors and their binding sites is therefore a major challenge in bioinformatics [1]. Advances in this field are expected to provide a basis for improving algorithmic binding site identification and promoter analysis [2], and for deciphering regulatory codes. Previous studies [3] have suggested that the information content deduced from binding site sequence sets ( ) approximately equals the information content deduced from relative binding site abundance ( ). Here, we investigate the relation between these two infor- mation quantities using a maximum entropy approach. 2 Outline of the Model We formally model