Finding transcriptional regulatory elements in Dictyostelium gene expression

In this paper, we proposed an improved method in the prediction of stage-specific TREs associated with four classes of developmentally regulated genes in Dictyostelium discoideum. TRE selection with a direct comparison of e-scores produced lots of the false positive results. In order to reduce false-positive prediction, we applied a normalization method to e-scores and predicted TREs in each developmentally regulated Dd gene sequence. Among the top 25 putative TREs in vegetative and culmination stage, we found two experimentally known TREs out of 6 known TREs in the TRANSFAC database. We also predicted five TREs experimentally known from the literature in the simulation results.