Apart from our observation, in transcriptional regulatory network, it has been pointed out in literature that TF signatures overlap poorly with their corresponding binding targets [5], possible explanations of which include protein-protein interactions between TFs [14], homology relationships [14], and indirect transcriptional regulation [5]. Our **data** and other studies indicate a substantial discrepancy between the biochemical networks and functional networks; explaining this contradictory behavior is an interesting question that we will address below.