title: Exploring comprehensive within-motif dependence of transcription factor binding in Escherichia coli.
abstract: Modeling the binding of transcription factors helps to decipher the control logic behind transcriptional regulatory networks. Position weight matrix is commonly used to describe a binding motif but assumes statistical independence between positions. Although current approaches take within-motif dependence into account for better predictive performance, these models usually rely on prior knowledge and incorporate simple positional dependence to describe binding motifs. The inability to take complex within-motif dependence into account may result in an incomplete representation of binding motifs. In this work, we applied association rule mining techniques and constructed models to explore within-motif dependence for transcription factors in Escherichia coli. Our models can reflect transcription factor-DNA recognition where the explored dependence correlates with the binding specificity. We also propose a graphical representation of the explored within-motif dependence to illustrate the final binding configurations. Understanding the binding configurations also enables us to fine-tune or design transcription factor binding sites, and we attempt to present the configurations through exploring within-motif dependence.
authors.affiliation: Institute of Biomedical Informatics, National Yang Ming University, Taipei, 11221, Taiwan.
authors.forename: Chi
authors.initials: C
authors.lastname: Yang
authors.affiliation: Institute of Biomedical Informatics, National Yang Ming University, Taipei, 11221, Taiwan.|Center for Systems and Synthetic Biology, National Yang Ming University, Taipei, 11221, Taiwan.
authors.forename: Chuan-Hsiung
authors.initials: CH
authors.lastname: Chang
mesh_terms: D001665:Binding Sites; D004269:DNA, Bacterial / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D057225:Data Mining; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial; D008969:Molecular Sequence Data; D059372:Nucleotide Motifs; D056510:Position-Specific Scoring Matrices; D011485:Protein Binding; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D004269:DNA, Bacterial; D029968:Escherichia coli Proteins; D014157:Transcription Factors