We report an application of machine learning algorithms that enables prediction of the functional context of transcription factor binding sites in the human genome. We demonstrate that our method allowed de novo identification of hepatic nuclear factor (HNF)4α binding sites and significantly improved an overall recognition of faithful HNF4α targets. When applied to published findings, an unprecedented high number of false positives were identified. The technique can be applied to any

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... on factor. The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2008/9/2/R36 Genome Biology 2008, 9:R36 http://genomebiology.com/2008/9/2/R36 Genome Biology 2008, Volume 9, Issue 2, Article R36 Kel et al. R36.2