Improved models for transcription factor binding site identification using nonindependent interactions.

@article{Zhao2012ImprovedMF,
  title={Improved models for transcription factor binding site identification using nonindependent interactions.},
  author={Yue Zhao and Shuxiang Ruan and Manishi Pandey and Gary D. Stormo},
  journal={Genetics},
  year={2012},
  volume={191 3},
  pages={781-90}
}
Identifying transcription factor (TF) binding sites is essential for understanding regulatory networks. The specificity of most TFs is currently modeled using position weight matrices (PWMs) that assume the positions within a binding site contribute independently to binding affinity for any site. Extensive, high-throughput quantitative binding assays let us examine, for the first time, the independence assumption for many TFs. We find that the specificity of most TFs is well fit with the simple… CONTINUE READING
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