Spatial signature scores are correlated with expression change in transcription factor deletion mutants.

<p>(A) Considering the top 50 target promoters predicted by each of four methods, ChIP-chip, our sequence signatures model, a simple thermodynamic model, and a single site model, we plot the number of cases in which that method’s predicted targets for a transcription factor exhibited a significantly different average expression upon deletion of the transcription factor. We shaded each bar by the number of times that, for a given method and transcription factor, the magnitude of this average expression difference ranked 1st (black), 2nd (dark gray), 3rd (light gray), or 4th (white) among the methods significantly associated with expression for that transcription factor. The targets predicted by the spatial signature model typically showed a greater magnitude of expression change upon factor deletion than did the targets predicted by the thermodynamic model (p = .0176, see Methods), which in turn typically exhibited a greater magnitude of expression change than those targets predicted by the single site model (p = .0005). (B) For each transcription factor where the top 50 predictions of ChIP-chip were associated with expression, we plot for each method the average expression change of its top 50 predicted targets upon that factor’s deletion. We derived 95% confidence intervals by resampling 5,000 sets of 50 putative targets chosen at random from the expression dataset and calculating the average expression change in each of these. Note that if the measured changes in expression are widespread, as is the case for the Nrg1 deletion, it is possible for the confidence interval derived from this null distribution to not contain zero.