ArticlePLoS genetics2012
Genome-wide location analysis reveals distinct transcriptional circuitry by paralogous regulators Foxa1 and Foxa2.
Article in PLoS genetics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers, 1 of them a synthesis that pooled it.
What it found
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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.
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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
35 citing papers in PubMed, 1 synthesis or guideline pooled it, 52 citations in OpenAlex.
- Comprehensive meta-analysis of Signal Transducers and Activators of Transcription (STAT) genomic binding patterns discerns cell-specific cis-regulatory modules.BMC genomics · 2013Pooled it
- Genome-wide rotational and translational phasing of nucleosomes with human transcription factors.Molecular cell · 2026Article
- FOXM1 cooperates with ERα to regulate functional β-cell mass.American journal of physiology. Endocrinology and metabolism · 2025Article
- Interrogating Estrogen Signaling Pathways in Human ER-Positive Breast Cancer Cells Forming Bone Metastases in Mice.Endocrinology · 2024Article
- Sequential ChIP-Seq.Methods in molecular biology (Clifton, N.J.) · 2024Article
- regioneReloaded: evaluating the association of multiple genomic region sets.Bioinformatics (Oxford, England) · 2023Article
- FOXA1 is a transcriptional activator of Odf2/Cenexin and regulates primary ciliation.Scientific reports · 2022Article
- Paralogous Genes Involved in Embryonic Development: Lessons from the Eye and Other Tissues.Genes · 2022Review
- The circRNA CNEACR regulates necroptosis of cardiomyocytes through Foxa2 suppression.Cell death and differentiation · 2022Article
- Article
- Resolving diverse protein-DNA footprints from exonuclease-based ChIP experiments.Bioinformatics (Oxford, England) · 2021Article
- Suppression of Cell Tumorigenicity by Non-neural Pro-differentiation Factors via Inhibition of Neural Property in Tumorigenic Cells.Frontiers in cell and developmental biology · 2021Article
- m6A RNA methylation-mediated HNF3γ reduction renders hepatocellular carcinoma dedifferentiation and sorafenib resistance.Signal transduction and targeted therapy · 2020Article
- Genome-Wide Analysis of the FOXA1 Transcriptional Network Identifies Novel Protein-Coding and Long Noncoding RNA Targets in Colorectal Cancer Cells.Molecular and cellular biology · 2020Article
- Functional informed genome-wide interaction analysis of body mass index, diabetes and colorectal cancer risk.Cancer medicine · 2020Article
- FOXA2 controls the cis-regulatory networks of pancreatic cancer cells in a differentiation grade-specific manner.The EMBO journal · 2019Article
- Article
- TRAP-seq identifies cystine/glutamate antiporter as a driver of recovery from liver injury.The Journal of clinical investigation · 2018Article
- DGCA: A comprehensive R package for Differential Gene Correlation Analysis.BMC systems biology · 2016Article
- Changes in Gene Expression and Estrogen Receptor Cistrome in Mouse Liver Upon Acute E2 Treatment.Molecular endocrinology (Baltimore, Md.) · 2016Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
Gene duplication is a powerful driver of evolution. Newly duplicated genes acquire new roles that are relevant to fitness, or they will be lost over time. A potential path to functional relevance is mutation of the coding sequence leading to the acquisition of novel biochemical properties, as analyzed here for the highly homologous paralogs Foxa1 and Foxa2 transcriptional regulators. We determine by genome-wide location analysis (ChIP-Seq) that, although Foxa1 and Foxa2 share a large fraction of binding sites in the liver, each protein also occupies distinct regulatory elements in vivo. Foxa1-only sites are enriched for p53 binding sites and are frequently found near genes important to cell cycle regulation, while Foxa2-restricted sites show only a limited match to the forkhead consensus and are found in genes involved in steroid and lipid metabolism. Thus, Foxa1 and Foxa2, while redundant during development, have evolved divergent roles in the adult liver, ensuring the maintenance of both genes during evolution.
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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.