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1.  Experimental strategies for studying transcription factor–DNA binding specificities 
Briefings in Functional Genomics  2010;9(5-6):362-373.
Specific binding of transcription factors (TFs) determines in a large part the connectivity of gene regulatory networks as well as the quantitative level of gene expression. A multiplicity of both experimental and computational methods is currently used to discover and characterize the underlying TF–DNA interactions. Experimental methods can be further subdivided into in vitro- and in vivo-based approaches, each accenting different aspects of TF-binding events. In this review we summarize the flexibility and performance of a selection of both types of experimental methods. In conclusion, we argue that a serial combination of methods with different throughput and data type constitutes an optimal experimental strategy.
doi:10.1093/bfgp/elq023
PMCID: PMC3080775  PMID: 20864494
transcription factor; DNA binding; binding affinity; ChIP; MITOMI; PBM; SELEX

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