Notwithstanding these limitations, we were able to reconstruct the dynamics of endotoxin-dependent transcription in human peripheral blood leukocytes using the above results. This included identifying the activity of ten transcription factors regulating expression of ninetynine genes. We also were able to identify additional genes that could be included in our model, notably 36 which had less initial evidence, but were substantiated by our predictions. Given that there were 1,215 genes with significant changes in gene expression for which regulatory relations were known, we were therefore able to capture between 8% (= 99 initial model genes/1,215 genes with significant expression changes and known regulatory relations) and 11% (99 + 36 additional genes = 135/1,215) of the explainable response. Furthermore, we were also able to identify new target genes based on the average gene expression profile of significant clusters, which could expand the scope of our temporal network still further. With a larger network reconstruction and **data** set specifically designed for use with NCA, it might be possible to move toward a nearcomplete characterization of dynamic transcription responses.