ArticleNPJ genomic medicine2020
Improved detection of tumor suppressor events in single-cell RNA-Seq data.
Article in NPJ genomic medicine, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 28 citations in OpenAlex.
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- Systematic design of combination therapy by targeting master regulators of coexisting diffuse midline glioma cell states.Nature genetics · 2026Article
- Multifaceted role of T-box transcription factor 4: From embryonic development to disease pathogenesis.Genes & diseases · 2026Review
- Comprehensive noise reduction in single-cell data with the RECODE platform.Cell reports methods · 2025Article
- Transposable element dynamics in glioblastoma stem cells: insights from locus-specific quantification.Mobile DNA · 2025Article
- Modeling combinatorial regulation from single-cell multi-omics provides regulatory units underpinning cell type landscape using cRegulon.Genome biology · 2025Article
- Scalable identification of lineage-specific gene regulatory networks from metacells with NetID.Genome biology · 2024Article
- Loss of coordination between basic cellular processes in human aging.Nature aging · 2024Article
- Matrix stiffness-dependent regulation of immunomodulatory genes in human MSCs is associated with the lncRNA CYTOR.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Molecular mechanisms reconstruction from single-cell multi-omics data with HuMMuS.Bioinformatics (Oxford, England) · 2024Article
- On epigenetic stochasticity, entropy and cancer risk.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2024Review
- Article
- Cell-attribute aware community detection improves differential abundance testing from single-cell RNA-Seq data.Nature communications · 2023Article
- Distance covariance entropy reveals primed states and bifurcation dynamics in single-cell RNA-Seq data.iScience · 2022Article
- Systematic identification of cell-fate regulatory programs using a single-cell atlas of mouse development.Nature genetics · 2022Article
- Inference of age-associated transcription factor regulatory activity changes in single cells.Nature aging · 2022Article
- Analysis of lung cancer-related genetic changes in long-term and low-dose polyhexamethylene guanidine phosphate (PHMG-p) treated human pulmonary alveolar epithelial cells.BMC pharmacology & toxicology · 2022Article
- decoupleR: ensemble of computational methods to infer biological activities from omics data.Bioinformatics advances · 2022Article
- Differential chromatin binding of the lung lineage transcription factor NKX2-1 resolves opposing murine alveolar cell fates in vivo.Nature communications · 2021Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Tissue-specific transcription factors are frequently inactivated in cancer. To fully dissect the heterogeneity of such tumor suppressor events requires single-cell resolution, yet this is challenging because of the high dropout rate. Here we propose a simple yet effective computational strategy called SCIRA to infer regulatory activity of tissue-specific transcription factors at single-cell resolution and use this tool to identify tumor suppressor events in single-cell RNA-Seq cancer studies. We demonstrate that tissue-specific transcription factors are preferentially inactivated in the corresponding cancer cells, suggesting that these are driver events. For many known or suspected tumor suppressors, SCIRA predicts inactivation in single cancer cells where differential expression does not, indicating that SCIRA improves the sensitivity to detect changes in regulatory activity. We identify NKX2-1 and TBX4 inactivation as early tumor suppressor events in normal non-ciliated lung epithelial cells from smokers. In summary, SCIRA can help chart the heterogeneity of tumor suppressor events at single-cell resolution.
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