ArticleCell reports2022
Uncovering the mesendoderm gene regulatory network through multi-omic data integration.
Article in Cell reports, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 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
11 citing papers in PubMed.
- TGFβ-dependent upregulation of OCIAD2 is essential for epithelial-to-mesenchymal transition during mesendoderm differentiation.Stem cell reports · 2026Article
- Foxh1 is a locus-specific PRC2 recruiter governing germ layer silencing.bioRxiv : the preprint server for biology · 2025Article
- Differentiation success of reprogrammed cells is heterogeneous in vivo and modulated by somatic cell identity memory.Stem cell reports · 2025Article
- The Trophoblast Compartment Helps Maintain Embryonic Pluripotency and Delays Differentiation towards Cardiomyocytes.International journal of molecular sciences · 2023Article
- FAM122A Is Required for Mesendodermal and Cardiac Differentiation of Embryonic Stem Cells.Stem cells (Dayton, Ohio) · 2023Article
- Quantitative analysis of transcriptome dynamics provides novel insights into developmental state transitions.BMC genomics · 2022Article
- Engagement of Foxh1 in chromatin regulation revealed by protein interactome analyses.Development, growth & differentiation · 2022Article
- Review
- Investigating chromatin accessibility during development and differentiation by ATAC-sequencing to guide the identification of cis-regulatory elements.Biochemical Society transactions · 2022Article
- Inferring causal gene regulatory networkFrontiers in bioengineering and biotechnology · 2022Article
- Control of zygotic genome activation in Xenopus.Current topics in developmental biology · 2021Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
16 authors.
Funding
Abstract
Mesendodermal specification is one of the earliest events in embryogenesis, where cells first acquire distinct identities. Cell differentiation is a highly regulated process that involves the function of numerous transcription factors (TFs) and signaling molecules, which can be described with gene regulatory networks (GRNs). Cell differentiation GRNs are difficult to build because existing mechanistic methods are low throughput, and high-throughput methods tend to be non-mechanistic. Additionally, integrating highly dimensional data composed of more than two data types is challenging. Here, we use linked self-organizing maps to combine chromatin immunoprecipitation sequencing (ChIP-seq)/ATAC-seq with temporal, spatial, and perturbation RNA sequencing (RNA-seq) data from Xenopus tropicalis mesendoderm development to build a high-resolution genome scale mechanistic GRN. We recover both known and previously unsuspected TF-DNA/TF-TF interactions validated through reporter assays. Our analysis provides insights into transcriptional regulation of early cell fate decisions and provides a general approach to building GRNs using highly dimensional multi-omic datasets.
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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.