Profiling the transcription factor regulatory networks of human cell types

Neph et al. (2012) (Circuitry and dynamics of human transcription factor regulatory networks. Cell, 150: 1274–1286) reported the transcription factor (TF) reg-ulatory networks of 41 human cell types using the DNaseI footprinting technique. This provides a valu-able resource for uncovering regulation principles in different human cells. In this paper, the architectures of the 41 regulatory networks and the distributions of housekeeping and specific regulatory interactions are investigated. The TF regulatory networks of dif-ferent human cell types demonstrate similar global three-layer (top, core and bottom) hierarchical archi-tectures, which are greatly different from the yeast TF regulatory network. However, they have distinguish-able local organizations, as suggested by the fact that wiring patterns of only a few TFs are enough to distinguish cell identities. The TF regulatory network of human embryonic stem cells (hESCs) is dense and enriched with interactions that are unseen in the net-works of other cell types. The examination of specific regulatory interactions suggests that specific inter-actions play important roles in hESCs