title: Profiling the transcription factor regulatory networks of human cell types.
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.
authors.affiliation: National Center for Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China.
authors.forename: Shihua
authors.initials: S
authors.lastname: Zhang
authors.affiliation: Department of Statistics and Applied Probability, National University of Singapore, Singapore 117546, Singapore.
authors.forename: Dechao
authors.initials: D
authors.lastname: Tian
authors.affiliation: Division of Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.
authors.forename: Ngoc Hieu
authors.initials: NH
authors.lastname: Tran
authors.affiliation: Department of Statistics and Applied Probability, National University of Singapore, Singapore 117546, Singapore Department of Mathematics, National University of Singapore, Singapore 119076, Singapore stackp@nus.edu.sg.
authors.forename: Kwok Pui
authors.initials: KP
authors.lastname: Choi
authors.affiliation: Department of Mathematics, National University of Singapore, Singapore 119076, Singapore National University of Singapore Graduate School for Integrative Sciences and Engineering, Singapore 117456, Singapore matzlx@nus.edu.sg.
authors.forename: Louxin
authors.initials: L
authors.lastname: Zhang
mesh_terms: D000465:Algorithms; D053595:Embryonic Stem Cells / Q000378:metabolism; D053263:Gene Regulatory Networks; D006801:Humans; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D014157:Transcription Factors