ArticleBMC genomics2008
Identification of Pou5f1, Sox2, and Nanog downstream target genes with statistical confidence by applying a novel algorithm to time course microarray and genome-wide chromatin immunoprecipitation data.
Article in BMC genomics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 105 papers, 2 of them syntheses that pooled it.
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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
105 citing papers in PubMed, 2 syntheses or guidelines pooled it, 164 citations in OpenAlex.
- Critical evaluation of transcription factor Atf2 as a candidate modulator of alcohol preference in mouse and human populations.Genetics and molecular research : GMR · 2013Pooled it
- BAY11 enhances OCT4 synthetic mRNA expression in adult human skin cells.Stem cell research & therapy · 2013Pooled it
- Functional interpretation of metabolomics data as a new method for predicting long-term side effects: treatment of atopic dermatitis in infants.Scientific reports · 2014Trial
- Systematic identification of Oct4 transcriptional targets in embryonic stem cells using the auxin-inducible degron system and nascent RNA sequencing.Cell regeneration (London, England) · 2025Article
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- A specific pluripotency-associated eRNA controls Nanog locus by shaping the epigenetic landscape and stabilizing enhancer-promoter interaction.Nucleic acids research · 2025Article
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- Endogenous retroviruses shape pluripotency specification in mouse embryos.Science advances · 2024Article
- Transcription factor binding sites are frequently under accelerated evolution in primates.Nature communications · 2023Article
- 5-azacytidine inhibits Sox2 promoter methylation during the induction of Thy-1American journal of translational research · 2023Article
- Cell-cell contact-driven EphB1 cis- and trans- signalings regulate cancer stem cells enrichment after chemotherapy.Cell death & disease · 2022Article
- Culture of Cancer Cells at Physiological Oxygen Levels Affects Gene Expression in a Cell-Type Specific Manner.Biomolecules · 2022Article
- The Defects of Epigenetic Reprogramming in Dox-Dependent Porcine-iPSCs.International journal of molecular sciences · 2022Article
- Atlas of regulated target genes of transcription factors (ART-TF) in human ES cells.BMC bioinformatics · 2022Article
- Review
- PI3Kδ activity controls plasticity and discriminates between EMT and stemness based on distinct TGFβ signaling.Communications biology · 2022Article
- Gadd45g initiates embryonic stem cell differentiation and inhibits breast cell carcinogenesis.Cell death discovery · 2021Article
- An Overview on the Complexity of OCT4: at the Level of DNA, RNA and Protein.Stem cell reviews and reports · 2021Review
- Article
- Dynamical reorganization of the pluripotency transcription factors Oct4 and Sox2 during early differentiation of embryonic stem cells.Scientific reports · 2020Article
45 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 1 institution in 1 country.
Funding
Abstract
backgroundTarget genes of a transcription factor (TF) Pou5f1 (Oct3/4 or Oct4), which is essential for pluripotency maintenance and self-renewal of embryonic stem (ES) cells, have previously been identified based on their response to Pou5f1 manipulation and occurrence of Chromatin-immunoprecipitation (ChIP)-binding sites in promoters. However, many responding genes with binding sites may not be direct targets because response may be mediated by other genes and ChIP-binding site may not be functional in terms of transcription regulation.
resultsTo reduce the number of false positives, we propose to separate responding genes into groups according to direction, magnitude, and time of response, and to apply the false discovery rate (FDR) criterion to each group individually. Using this novel algorithm with stringent statistical criteria (FDR < 0.2) to a compendium of published and new microarray data (3, 6, 12, and 24 hr after Pou5f1 suppression) and published ChIP data, we identified 420 tentative target genes (TTGs) for Pou5f1. The majority of TTGs (372) were down-regulated after Pou5f1 suppression, indicating that the Pou5f1 functions as an activator of gene expression when it binds to promoters. Interestingly, many activated genes are potent suppressors of transcription, which include polycomb genes, zinc finger TFs, chromatin remodeling factors, and suppressors of signaling. Similar analysis showed that Sox2 and Nanog also function mostly as transcription activators in cooperation with Pou5f1.
conclusionWe have identified the most reliable sets of direct target genes for key pluripotency genes - Pou5f1, Sox2, and Nanog, and found that they predominantly function as activators of downstream gene expression. Thus, most genes related to cell differentiation are suppressed indirectly.
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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.