Figure 2

Experimental verification of putative FoxA sites by EMSA. A – EMSA competition of oligonucleotides containing predicted FoxA sites, with labeled TTR probe for binding to recombinant GST-FKH-FoxA2 (demonstrative autoradiographs). The ascending concentrations (2, 5, and 20 ng) of cold competitors are shown as triangles at the top of the figure, their IDs and resulting relative EMSA scores are shown at the bottom. The band corresponding to the DNA-protein complex is marked by the arrow. Unlabeled TTR and PPAR oligonucleotides were used as positive and negative controls of protein binding. B – Distribution of EMSA scores for 64 potential FoxA binding sites selected for EMSA verification. Selected BSs had peak height of at least 15 and were located in 1000 bp upstream regions of RefSeq genes. The X and Y axes denote the EMSA score and the number of sites predicted at a specific EMSA-score threshold. EMSA scores are rough estimates of TFBS affinities relative to that of the positive control site (referred to as the EMSA scores listed in Additional file 1: Table S1). White, grey and black columns denote the EMSA scores below 0.25 (non-sites), 0.25 to 0.75 (weak sites) and above 0.75 (strong sites).