Figure 5

The PAP regulon. Comparison of the expression of the CERMT predicted regulon (upper panel) and the over-expression defined regulon [47] (lower panel) versus the expression of the PAP1 transcription factor in the shoot in response to salt and osmotic stress. No time lag was used for the prediction, so there is no overlap between predicted and true regulons. The difference in terms of coherency and variance is pronounced so it is not hard to see why the algorithm is seeded with no time lag instead of the more appropriate lag of two time points. This illustrates an unavoidable problem of TF target prediction based only on gene expression data – there are no unique solutions and the most obvious solution is not necessarily the correct one.