ArticleNature communications2018
Transcriptional synergy as an emergent property defining cell subpopulation identity enables population shift.
Article in Nature communications, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Redefining cellular reprogramming with advanced genomic technologies.Nature reviews. Genetics · 2026Review
- Accurate Transcription Factor Activity Inference to Decipher Cell Identity from Single-Cell Transcriptomic Data with MetaTF.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Molecular logic for cellular specializations that initiate the auditory parallel processing pathways.Nature communications · 2025Article
- Molecular logic for cellular specializations that initiate the auditory parallel processing pathways.bioRxiv : the preprint server for biology · 2024Article
- Transcriptional synergy in human aortic endothelial cells is vulnerable to combination p300/CBP and BET bromodomain inhibition.iScience · 2024Article
- Computational Methods to Identify Cell-Fate Determinants, Identity Transcription Factors, and Niche-Induced Signaling Pathways for Stem Cell Research.Methods in molecular biology (Clifton, N.J.) · 2022Article
- TransSynW: A single-cell RNA-sequencing based web application to guide cell conversion experiments.Stem cells translational medicine · 2021Article
- Computational Stem Cell Biology: Open Questions and Guiding Principles.Cell stem cell · 2021Review
- Microglial subtypes: diversity within the microglial community.The EMBO journal · 2019Review
- Crosstalk of Intercellular Signaling Pathways in the Generation of Midbrain Dopaminergic Neurons In Vivo and from Stem Cells.Journal of developmental biology · 2019Review
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Single-cell RNA sequencing allows defining molecularly distinct cell subpopulations. However, the identification of specific sets of transcription factors (TFs) that define the identity of these subpopulations remains a challenge. Here we propose that subpopulation identity emerges from the synergistic activity of multiple TFs. Based on this concept, we develop a computational platform (TransSyn) for identifying synergistic transcriptional cores that determine cell subpopulation identities. TransSyn leverages single-cell RNA-seq data, and performs a dynamic search for an optimal synergistic transcriptional core using an information theoretic measure of synergy. A large-scale TransSyn analysis identifies transcriptional cores for 186 subpopulations, and predicts identity conversion TFs between 3786 pairs of cell subpopulations. Finally, TransSyn predictions enable experimental conversion of human hindbrain neuroepithelial cells into medial floor plate midbrain progenitors, capable of rapidly differentiating into dopaminergic neurons. Thus, TransSyn can facilitate designing strategies for conversion of cell subpopulation identities with potential applications in regenerative medicine.
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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.