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- Title
Evaluation of methods for modeling transcription factor sequence specificity.
- Authors
Weirauch, Matthew T; Cote, Atina; Norel, Raquel; Annala, Matti; Zhao, Yue; Riley, Todd R; Saez-Rodriguez, Julio; Cokelaer, Thomas; Vedenko, Anastasia; Talukder, Shaheynoor; Agius, Phaedra; Arvey, Aaron; Bucher, Philipp; Callan, Curtis G; Chang, Cheng Wei; Chen, Chien-Yu; Chen, Yong-Syuan; Chu, Yu-Wei; Grau, Jan; Grosse, Ivo
- Abstract
Genomic analyses often involve scanning for potential transcription factor (TF) binding sites using models of the sequence specificity of DNA binding proteins. Many approaches have been developed to model and learn a protein's DNA-binding specificity, but these methods have not been systematically compared. Here we applied 26 such approaches to in vitro protein binding microarray data for 66 mouse TFs belonging to various families. For nine TFs, we also scored the resulting motif models on in vivo data, and found that the best in vitro-derived motifs performed similarly to motifs derived from the in vivo data. Our results indicate that simple models based on mononucleotide position weight matrices trained by the best methods perform similarly to more complex models for most TFs examined, but fall short in specific cases (<10% of the TFs examined here). In addition, the best-performing motifs typically have relatively low information content, consistent with widespread degeneracy in eukaryotic TF sequence preferences.
- Subjects
TRANSCRIPTION factors; NUCLEOTIDE sequence; CARRIER proteins; DNA-binding proteins; COMPARATIVE studies; DNA microarrays
- Publication
Nature Biotechnology, 2013, Vol 31, Issue 2, p126
- ISSN
1087-0156
- Publication type
Article
- DOI
10.1038/nbt.2486