ArticleDevelopment (Cambridge, England)2014
Machine learning classification of cell-specific cardiac enhancers uncovers developmental subnetworks regulating progenitor cell division and cell fate specification.
Article in Development (Cambridge, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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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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Who cites it
23 citing papers in PubMed, 33 citations in OpenAlex.
- Article
- trithorax is an essential regulator of cardiac Hox gene expression and anterior-posterior patterning of the Drosophila embryonic heart tube.Biology open · 2025Article
- Genome-Wide Expression Profiling and Phenotypic Analysis of Downstream Targets Identify the Fox Transcription Factor Jumeau as a Master Regulator of Cardiac Progenitor Cell Division.International journal of molecular sciences · 2024Article
- c-JUN is a barrier in hESC to cardiomyocyte transition.Life science alliance · 2023Article
- Machine learning-based detection of label-free cancer stem-like cell fate.Scientific reports · 2022Article
- A regulatory network of Sox and Six transcription factors initiate a cell fate transformation during hearing regeneration in adult zebrafish.Cell genomics · 2022Article
- Assessing the Roles of Potential Notch Signaling Components in Instructive and Permissive Pathways with Two Drosophila Pericardial Reporters.Methods in molecular biology (Clifton, N.J.) · 2022Article
- The Drosophila Forkhead/Fox transcription factor Jumeau mediates specific cardiac progenitor cell divisions by regulating expression of the kinesin Nebbish.Scientific reports · 2021Article
- Heart Enhancers: Development and Disease Control at a Distance.Frontiers in genetics · 2021Review
- Article
- A population of adult satellite-like cells ineLife · 2018Article
- Conserved signaling mechanisms in Drosophila heart development.Developmental dynamics : an official publication of the American Association of Anatomists · 2017Review
- Challenges and progress in interpretation of non-coding genetic variants associated with human disease.Experimental biology and medicine (Maywood, N.J.) · 2017Article
- A novel method for predicting activity of cis-regulatory modules, based on a diverse training set.Bioinformatics (Oxford, England) · 2017Article
- Prediction and validation of protein-protein interactors from genome-wide DNA-binding data using a knowledge-based machine-learning approach.Open biology · 2016Article
- Genome-Wide Approaches to Drosophila Heart Development.Journal of cardiovascular development and disease · 2016Article
- Two Forkhead transcription factors regulate cardiac progenitor specification by controlling the expression of receptors of the fibroblast growth factor and Wnt signaling pathways.Development (Cambridge, England) · 2016Article
- The myogenic repressor gene Holes in muscles is a direct transcriptional target of Twist and Tinman in the Drosophila embryonic mesoderm.Developmental biology · 2015Article
- Extrapolating histone marks across developmental stages, tissues, and species: an enhancer prediction case study.BMC genomics · 2015Article
- Enhancer modeling uncovers transcriptional signatures of individual cardiac cell states in Drosophila.Nucleic acids research · 2015Article
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Authors and funding
11 authors at 5 institutions in 1 country.
Funding
Abstract
The Drosophila heart is composed of two distinct cell types, the contractile cardial cells (CCs) and the surrounding non-muscle pericardial cells (PCs), development of which is regulated by a network of conserved signaling molecules and transcription factors (TFs). Here, we used machine learning with array-based chromatin immunoprecipitation (ChIP) data and TF sequence motifs to computationally classify cell type-specific cardiac enhancers. Extensive testing of predicted enhancers at single-cell resolution revealed the added value of ChIP data for modeling cell type-specific activities. Furthermore, clustering the top-scoring classifier sequence features identified novel cardiac and cell type-specific regulatory motifs. For example, we found that the Myb motif learned by the classifier is crucial for CC activity, and the Myb TF acts in concert with two forkhead domain TFs and Polo kinase to regulate cardiac progenitor cell divisions. In addition, differential motif enrichment and cis-trans genetic studies revealed that the Notch signaling pathway TF Suppressor of Hairless [Su(H)] discriminates PC from CC enhancer activities. Collectively, these studies elucidate molecular pathways used in the regulatory decisions for proliferation and differentiation of cardiac progenitor cells, implicate Su(H) in regulating cell fate decisions of these progenitors, and document the utility of enhancer modeling in uncovering developmental regulatory subnetworks.
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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.