ArticleMolecular systems biology2023
GRaNIE and GRaNPA: inference and evaluation of enhancer-mediated gene regulatory networks.
Article in Molecular systems biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed, 61 citations in OpenAlex.
- Inferring Gene Regulatory Networks in Stem Cells: Methods and Applications.Methods in molecular biology (Clifton, N.J.) · 2027Review
- T-ChroNet: Time-aware chromatin network reconstruction to detect dynamic regulatory programs in longitudinal epigenetic dataset.NAR genomics and bioinformatics · 2026Article
- Rare regulatory mutations disrupt mesenchymal molecular programs driving endocardial cushion formation in bicuspid aortic valve.Nature communications · 2026Article
- Acquisition and extinction of drug-context memories are linked to distinct epigenetic and transcriptional mechanisms in the mouse dentate gyrus.bioRxiv : the preprint server for biology · 2026Article
- BARTsc identifies key transcriptional regulators from single-cell omics data.bioRxiv : the preprint server for biology · 2026Article
- IFNγ shapes macrophage inflammatory responses by STAT1 isoform-specific epigenetic and transcriptional mechanisms.BMC genomics · 2026Article
- The evolution of gene regulation in mammalian cerebellum development.Science (New York, N.Y.) · 2026Article
- Spatially resolved integrative analysis of transcriptomic and metabolomic changes in tissue injury studies.Nature communications · 2026Article
- Modeling strategies forBioinformatics advances · 2026Article
- DANSE: a pipeline for dynamic modelling of time-series multi-omics data.BMC bioinformatics · 2025Article
- Mutational disruption of transcription factors binding and regulatory networks in a case of unexplained total fertilization failure.Journal of translational medicine · 2025Article
- Multi-omic network inference from time-series data.NPJ systems biology and applications · 2025Article
- A noncanonical role of glycolytic metabolites controlling the timing of mouse embryo segmentation.Science advances · 2025Article
- Epiregulon: Single-cell transcription factor activity inference to predict drug response and drivers of cell states.Nature communications · 2025Article
- Leveraging transcription factor physical proximity for enhancing gene regulation inference.Bioinformatics (Oxford, England) · 2025Article
- Single-cell ultra-high-throughput multiplexed chromatin and RNA profiling reveals gene regulatory dynamics.Nature methods · 2025Article
- Active repression of cell fate plasticity by PROX1 safeguards hepatocyte identity and prevents liver tumorigenesis.Nature genetics · 2025Article
- Leveraging prior knowledge to infer gene regulatory networks from single-cell RNA-sequencing data.Molecular systems biology · 2025Review
- Review
- Chromatin enables precise and scalable gene regulation with factors of limited specificity.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
15 authors at 2 institutions in 2 countries.
Funding
Abstract
Enhancers play a vital role in gene regulation and are critical in mediating the impact of noncoding genetic variants associated with complex traits. Enhancer activity is a cell-type-specific process regulated by transcription factors (TFs), epigenetic mechanisms and genetic variants. Despite the strong mechanistic link between TFs and enhancers, we currently lack a framework for jointly analysing them in cell-type-specific gene regulatory networks (GRN). Equally important, we lack an unbiased way of assessing the biological significance of inferred GRNs since no complete ground truth exists. To address these gaps, we present GRaNIE (Gene Regulatory Network Inference including Enhancers) and GRaNPA (Gene Regulatory Network Performance Analysis). GRaNIE (https://git.embl.de/grp-zaugg/GRaNIE) builds enhancer-mediated GRNs based on covariation of chromatin accessibility and RNA-seq across samples (e.g. individuals), while GRaNPA (https://git.embl.de/grp-zaugg/GRaNPA) assesses the performance of GRNs for predicting cell-type-specific differential expression. We demonstrate their power by investigating gene regulatory mechanisms underlying the response of macrophages to infection, cancer and common genetic traits including autoimmune diseases. Finally, our methods identify the TF PURA as a putative regulator of pro-inflammatory macrophage polarisation.
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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.