ArticleStem cells (Dayton, Ohio)2015
Interrogation of a context-specific transcription factor network identifies novel regulators of pluripotency.
Article in Stem cells (Dayton, Ohio), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
21 citing papers in PubMed, 38 citations in OpenAlex.
- The regulatory architecture of the primed pluripotent cell state.Nature communications · 2025Article
- Sox2 interacts with Atoh1 and Huwe1 loci to regulate Atoh1 transcription and stability during hair cell differentiation.PLoS genetics · 2025Article
- Transcription factor network analysis identifies REST/NRSF as an intrinsic regulator of CNS regeneration in mice.Nature communications · 2022Article
- Review
- Article
- The Master Regulator Protein BAZ2B Can Reprogram Human Hematopoietic Lineage-Committed Progenitors into a Multipotent State.Cell reports · 2020Article
- Nuclear gene proximity and protein interactions shape transcript covariations in mammalian single cells.Nature communications · 2020Article
- Racial Differences in the Association Between Luminal Master Regulator Gene Expression Levels and Breast Cancer Survival.Clinical cancer research : an official journal of the American Association for Cancer Research · 2020Article
- Impact of Teratoma on the Cumulative Incidence of Disease-Related Death in Patients With Advanced Germ Cell Tumors.Journal of clinical oncology : official journal of the American Society of Clinical Oncology · 2019Article
- A network-based approach to identify DNA methylation and its involved molecular pathways in testicular germ cell tumors.Journal of Cancer · 2019Article
- Quantitative assessment of protein activity in orphan tissues and single cells using the metaVIPER algorithm.Nature communications · 2018Article
- TCF7L1 suppresses primitive streak gene expression to support human embryonic stem cell pluripotency.Development (Cambridge, England) · 2018Article
- Modeling signaling-dependent pluripotency with Boolean logic to predict cell fate transitions.Molecular systems biology · 2018Article
- OCT4 impedes cell fate redirection by the melanocyte lineage master regulator MITF in mouse ESCs.Nature communications · 2017Article
- An Integrated Systems Biology Approach Identifies TRIM25 as a Key Determinant of Breast Cancer Metastasis.Cell reports · 2017Article
- Inference of cell type specific regulatory networks on mammalian lineages.Current opinion in systems biology · 2017Article
- The recurrent architecture of tumour initiation, progression and drug sensitivity.Nature reviews. Cancer · 2017Review
- Functional characterization of somatic mutations in cancer using network-based inference of protein activity.Nature genetics · 2016Article
- Mechanism and Role of SOX2 Repression in Seminoma: Relevance to Human Germline Specification.Stem cell reports · 2016Article
- Functional annotation of the vlinc class of non-coding RNAs using systems biology approach.Nucleic acids research · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
18 authors at 2 institutions in 1 country.
Funding
Abstract
The predominant view of pluripotency regulation proposes a stable ground state with coordinated expression of key transcription factors (TFs) that prohibit differentiation. Another perspective suggests a more complexly regulated state involving competition between multiple lineage-specifying TFs that define pluripotency. These contrasting views were developed from extensive analyses of TFs in pluripotent cells in vitro. An experimentally validated, genome-wide repertoire of the regulatory interactions that control pluripotency within the in vivo cellular contexts is yet to be developed. To address this limitation, we assembled a TF interactome of adult human male germ cell tumors (GCTs) using the Algorithm for the Accurate Reconstruction of Cellular Pathways (ARACNe) to analyze gene expression profiles of 141 tumors comprising pluripotent and differentiated subsets. The network (GCT(Net)) comprised 1,305 TFs, and its ingenuity pathway analysis identified pluripotency and embryonal development as the top functional pathways. We experimentally validated GCT(Net) by functional (silencing) and biochemical (ChIP-seq) analysis of the core pluripotency regulatory TFs POU5F1, NANOG, and SOX2 in relation to their targets predicted by ARACNe. To define the extent of the in vivo pluripotency network in this system, we ranked all TFs in the GCT(Net) according to sharing of ARACNe-predicted targets with those of POU5F1 and NANOG using an odds-ratio analysis method. To validate this network, we silenced the top 10 TFs in the network in H9 embryonic stem cells. Silencing of each led to downregulation of pluripotency and induction of lineage; 7 of the 10 TFs were identified as pluripotency regulators for the first time.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.