ArticlePloS one2014
Boolean modelling reveals new regulatory connections between transcription factors orchestrating the development of the ventral spinal cord.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Article
- Gene2role: a role-based gene embedding method for comparative analysis of signed gene regulatory networks.BMC bioinformatics · 2025Article
- COFFEE: consensus single cell-type specific inference for gene regulatory networks.Briefings in bioinformatics · 2024Article
- COFFEE: Consensus Single Cell-Type Specific Inference for Gene Regulatory Networks.bioRxiv : the preprint server for biology · 2024Article
- Approaches for Benchmarking Single-Cell Gene Regulatory Network Methods.Bioinformatics and biology insights · 2024Review
- Modulating the dynamics of NFκB and PI3K enhances the ensemble-level TNFR1 signaling mediated apoptotic response.NPJ systems biology and applications · 2023Article
- Inferring gene regulatory network from single-cell transcriptomes with graph autoencoder model.PLoS genetics · 2023Article
- On the Consistency between Gene Expression and the Gene Regulatory Network ofNetwork and systems medicine · 2021Article
- Canonical Wnt/β-catenin activity and differential epigenetic marks direct sexually dimorphic regulation ofDevelopment (Cambridge, England) · 2020Article
- Benchmarking algorithms for gene regulatory network inference from single-cell transcriptomic data.Nature methods · 2020Article
- Analysis on gene modular network reveals morphogen-directed development robustness inCell discovery · 2020Article
- E. coli gene regulatory networks are inconsistent with gene expression data.Nucleic acids research · 2019Article
- Neural Progenitors Adopt Specific Identities by Directly Repressing All Alternative Progenitor Transcriptional Programs.Developmental cell · 2016Article
- In Silico Gene Regulatory Network of the Maurer's Cleft Pathway in Plasmodium falciparum.Evolutionary bioinformatics online · 2015Article
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7 authors.
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Abstract
We have assembled a network of cell-fate determining transcription factors that play a key role in the specification of the ventral neuronal subtypes of the spinal cord on the basis of published transcriptional interactions. Asynchronous Boolean modelling of the network was used to compare simulation results with reported experimental observations. Such comparison highlighted the need to include additional regulatory connections in order to obtain the fixed point attractors of the model associated with the five known progenitor cell types located in the ventral spinal cord. The revised gene regulatory network reproduced previously observed cell state switches between progenitor cells observed in knock-out animal models or in experiments where the transcription factors were overexpressed. Furthermore the network predicted the inhibition of Irx3 by Nkx2.2 and this prediction was tested experimentally. Our results provide evidence for the existence of an as yet undescribed inhibitory connection which could potentially have significance beyond the ventral spinal cord. The work presented in this paper demonstrates the strength of Boolean modelling for identifying gene regulatory networks.
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