ArticleNucleic acids research2014
Profiling the transcription factor regulatory networks of human cell types.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Transcriptional regulatory network analysis uncovers modular gene control and potential key regulators in diabetic cardiomyopathy.Frontiers in cell and developmental biology · 2026Article
- Discovery of therapeutic targets in cancer using chromatin accessibility and transcriptomic data.Cell systems · 2024Article
- Spontaneously evolved progenitor niches escape Yap oncogene addiction in advanced pancreatic ductal adenocarcinomas.Nature communications · 2023Article
- Indirect Mechanisms of Transcription Factor-Mediated Gene Regulation during Cell Fate Changes.Advanced genetics (Hoboken, N.J.) · 2022Article
- Joint reconstruction of cis-regulatory interaction networks across multiple tissues using single-cell chromatin accessibility data.Briefings in bioinformatics · 2021Article
- Core transcriptional regulatory circuitries in cancer.Oncogene · 2020Review
- TopicNet: a framework for measuring transcriptional regulatory network change.Bioinformatics (Oxford, England) · 2020Article
- LncMAP: Pan-cancer atlas of long noncoding RNA-mediated transcriptional network perturbations.Nucleic acids research · 2018Article
- Estimating the effects of transcription factors binding and histone modifications on gene expression levels in human cells.Oncotarget · 2017Article
- Comparison of tissue/disease specific integrated networks using directed graphlet signatures.BMC bioinformatics · 2017Article
- Integrative Analysis of Transcription Factor Combinatorial Interactions Using a Bayesian Tensor Factorization Approach.Frontiers in genetics · 2017Article
- Identifying gene regulatory network rewiring using latent differential graphical models.Nucleic acids research · 2016Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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