Profiling the transcription factor regulatory networks of human cell types. Issue 20 (9th October 2014)

• Record Type: Journal Article
• Authors: Zhang, Shihua; Tian, Dechao; Tran, Ngoc Hieu; Choi, Kwok Pui; Zhang, Louxin
• Is Part Of: Nucleic acids research. Volume 42:Issue 20(2014)
• Page Start: 12380
• Page End: 12387
• Publication Date: 2014-10-09
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gku923
• Languages: English
• ISSNs: 0305-1048

Abstract

Abstract: Neph et al. (2012) (Circuitry and dynamics of human transcription factor regulatory networks. Cell, 150: 1274–1286) reported the transcription factor (TF) regulatory networks of 41 human cell types using the DNaseI footprinting technique. This provides a valuable 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 different human cell types demonstrate similar global three-layer (top, core and bottom) hierarchical architectures, which are greatly different from the yeast TF regulatory network. However, they have distinguishable 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 networks of other cell types. The examination of specific regulatory interactions suggests that specific interactions play important roles in hESCs.