ArticleiScience2022
miRSCAPE - inferring miRNA expression from scRNA-seq data.
Article in iScience, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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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
15 citing papers in PubMed.
- Fluctuating environment causes neoplastic transition and epithelial-mesenchymal plasticity in human cells.Research square · 2026Article
- miRSiC: a regulatory-aware machine learning framework for microRNA expression inference across bulk and single-cell transcriptomes.Briefings in bioinformatics · 2026Article
- Target-site dynamics explain a large share of apparent microRNA differential expression.RNA (New York, N.Y.) · 2026Article
- Construction of a Computationally Inferred Single-Cell miRNA Activity Atlas and Analysis of Regulatory Networks in Spinal Cord Injury.Journal of molecular neuroscience : MN · 2026Article
- SiCmiR Atlas: Single-Cell miRNA Landscape Reveals Hub-miRNA and Network Signatures in Human Cancers.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- bayesReact: expression-coupled regulatory motif analysis detects microRNA activity across cancers, tissues, and at the single-cell level.Nucleic acids research · 2026Article
- Evaluating Genetic Regulators of MicroRNAs Using Machine Learning Models.International journal of molecular sciences · 2025Article
- Inferring single-cell and spatial microRNA activity from transcriptomics data.Communications biology · 2025Article
- STmiR: A Novel XGBoost-based framework for spatially resolved miRNA activity prediction in cancer transcriptomics.PloS one · 2025Article
- Using deep neural networks and LASSO regression to predict miRNA expression changes based on mRNA data.Frontiers in bioinformatics · 2025Article
- AAAGUGC Seed-Containing miRNAs: Master Regulators of Cancer Pathways and Therapeutic Resistance.MicroRNA (Shariqah, United Arab Emirates) · 2025Review
- Epigenetic Biomarkers in Thrombophilia-Related Pregnancy Complications: Mechanisms, Diagnostic Potential, and Therapeutic Implications: A Narrative Review.International journal of molecular sciences · 2024Review
- SingmiR: a single-cell miRNA alignment and analysis tool.Nucleic acids research · 2024Article
- Advances in applications of artificial intelligence algorithms for cancer-related miRNA research.Zhejiang da xue xue bao. Yi xue ban = Journal of Zhejiang University. Medical sciences · 2024Review
- Noncoding RNA circuitry in melanoma onset, plasticity, and therapeutic response.Pharmacology & therapeutics · 2023Review
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Our understanding of miRNA activity at cellular resolution is thwarted by the inability of standard scRNA-seq protocols to capture miRNAs. We introduce a novel tool, miRSCAPE, to infer miRNA expression in a sample from its RNA-seq profile. We establish miRSCAPE's accuracy in 10 tumor and normal cohorts demonstrating its superiority over alternatives. miRSCAPE accurately infers cell type-specific miRNA activities (predicted versus observed fold-difference correlation ∼0.81) in two independent scRNA-seq datasets. We apply miRSCAPE to infer miRNA activities in scRNA clusters in pancreatic and lung adenocarcinomas, as well as in 56 cell types in the human cell landscape (HCL). In pancreatic and breast cancer scRNA-seq data, miRSCAPE recapitulates miRNAs associated with stemness and epithelial-mesenchymal transition (EMT) cell states, respectively. Overall, miRSCAPE recapitulates and refines miRNA biology at cellular resolution. miRSCAPE is freely available and is easily applicable to scRNA-seq data to infer miRNA activities at cellular resolution.
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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.