Geertz, MarcelMaerkl, Sebastian J.2011-01-172011-01-172011-01-17201010.1093/bfgp/elq023https://infoscience.epfl.ch/handle/20.500.14299/63022WOS:000286675100002Specific 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.transcription factorDNA bindingbinding affinityChIPMitomiPbmSelexSurface-Plasmon ResonanceProtein-DnaGene-RegulationIn-VivoRegulatory NetworksChromatin-ImmunoprecipitationSaccharomyces-CerevisiaeGel-ElectrophoresisZinc FingersGenometext::journal::journal article::review article