Bioinformatics. 2012 Jan 1;28(1):56-62. doi:
10.1093/bioinformatics/btr614. Epub 2011 Nov 8.
Epigenetic priors for identifying active transcription factor binding sites. Cuellar-Partida G, Buske FA, McLeay RC, Whitington T, Noble WS, Bailey TL.
Score (posterior, at position i in the genome) = PWM for TF t at position i + priors at i (H3K4me + Dnase), gets 60% sens. at FPR of 1% averaged over all i & t, using essentially equal weighting on each functional genomics track. One issue here is because of the huge size of the genome the 1% FPR actually turns into a very low PPV, giving 5 FPs for each TP in practice.
http://www.ncbi.nlm.nih.gov/pubmed/22072382
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