ArticleCell systems2020
Conserved Epigenetic Regulatory Logic Infers Genes Governing Cell Identity.
Article in Cell systems, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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.
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
26 citing papers in PubMed, 49 citations in OpenAlex.
- TRIAGE Toolkit: Streamlined Discovery of Regulatory Genes and Elements.Current protocols · 2026Article
- Computational modelling of cell identity.The Biochemical journal · 2026Review
- The changing landscape of gene expression analysis.Briefings in bioinformatics · 2026Review
- A pluripotent stem cell atlas of multilineage differentiation.Scientific data · 2025Article
- Refate identifies chemical compounds to target trans-regulatory networks for cellular conversion.bioRxiv : the preprint server for biology · 2025Article
- Single-cell multi-omics delineates the dynamics of distinct epigenetic codes coordinating mouse gastrulation.BMC genomics · 2025Article
- Atlas of multilineage stem cell differentiation reveals TMEM88 as a developmental regulator of blood pressure.Nature communications · 2025Article
- Systematic analysis of the transcriptional landscape of melanoma reveals drug-target expression plasticity.Briefings in functional genomics · 2025Article
- TRIAGE: an R package for regulatory gene analysis.Briefings in bioinformatics · 2025Article
- Putative epigenetic regulation mechanisms related to production, carcass and beef quality traits in Nelore cattle.Frontiers in genetics · 2025Article
- Cooperative insulation of regulatory domains by CTCF-dependent physical insulation and promoter competition.Nature communications · 2024Article
- TGF-β modulates cell fate in human ES cell-derived foregut endoderm by inhibiting Wnt and BMP signaling.Stem cell reports · 2024Article
- Epigenetic regulation of complement C1Q gene expression.Frontiers in immunology · 2024Article
- Evaluation of deep learning-based feature selection for single-cell RNA sequencing data analysis.Genome biology · 2023Article
- Tbx5 maintains atrial identity in post-natal cardiomyocytes by regulating an atrial-specific enhancer network.Nature cardiovascular research · 2023Article
- Low RNA stability signifies increased post-transcriptional regulation of cell identity genes.Nucleic acids research · 2023Article
- Inferring cell diversity in single cell data using consortium-scale epigenetic data as a biological anchor for cell identity.Nucleic acids research · 2023Article
- A transposable element into the human long noncoding RNA CARMEN is a switch for cardiac precursor cell specification.Cardiovascular research · 2023Article
- POSTRE: a tool to predict the pathological effects of human structural variants.Nucleic acids research · 2023Article
- Repressive epigenetic mechanisms, such as the H3K27me3 histone modification, were predicted to affect muscle gene expression and its mineral content in Nelore cattle.Biochemistry and biophysics reports · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
21 authors at 9 institutions in 3 countries.
Funding
Abstract
Determining genes that orchestrate cell differentiation in development and disease remains a fundamental goal of cell biology. This study establishes a genome-wide metric based on the gene-repressive trimethylation of histone H3 at lysine 27 (H3K27me3) across hundreds of diverse cell types to identify genetic regulators of cell differentiation. We introduce a computational method, TRIAGE, which uses discordance between gene-repressive tendency and expression to identify genetic drivers of cell identity. We apply TRIAGE to millions of genome-wide single-cell transcriptomes, diverse omics platforms, and eukaryotic cells and tissue types. Using a wide range of data, we validate the performance of TRIAGE in identifying cell-type-specific regulatory factors across diverse species including human, mouse, boar, bird, fish, and tunicate. Using CRISPR gene editing, we use TRIAGE to experimentally validate RNF220 as a regulator of Ciona cardiopharyngeal development and SIX3 as required for differentiation of endoderm in human pluripotent stem cells. A record of this paper's transparent peer review process is included in the Supplemental Information.
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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.