Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches

A comparison of the distribution of binding sites that (1) contain a conventional OCT consensus (ATGC[A/T]AAT); (2) lack the consensus but contain a match to the OCT PWM identified by the ChIPMotifs approach with 1.0 > S_{c_h} ≥ 0.88 and 0.95 > S_{p_h} ≥ 0.85 (the consensus sites would have also been identified by the OCT PWM but have not been included in this set for comparison purposes); and (3) contain no match to the OCT PWM above S_{c_h} 0.88, S_{p_h} 0.85. The OCT4-binding regions were defined as peaks detected on duplicate ENCODE arrays using a peak calling program developed for ChIP-chip experiments (Bieda et al. 2006); the gene list was based on GENCODE Genes (Harrow et al. 2006).