ArticlePatterns (New York, N.Y.)2022
scTenifoldKnk: An efficient virtual knockout tool for gene function predictions via single-cell gene regulatory network perturbation.
Article in Patterns (New York, N.Y.), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 217 papers.
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Who cites it
217 citing papers in PubMed.
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- Cadmium Exposure and Osteoporosis: A Spatially Contextualized Adverse Outcome Pathway Integrating Epidemiology, Toxicogenomics and Transcriptomics.Biological trace element research · 2026Article
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- Single-Cell Mapping Identifies Aging-Associated Neutrophil Remodeling Across Multiple Organs.Aging cell · 2026Article
- Unveiling the Diagnostic Value and Potential Therapeutic Targets of Phenylalanine Metabolism in Pancreatic Cancer via Integrated Multi-Omics and Machine Learning.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2026Article
- Integrated Multi-Omics Reveals Cellular States and Microenvironmental Remodeling in Coexisting DCIS and IDC.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- DONSON links tumor-cell survival to MIF-associated macrophage remodeling in small cell lung cancer.Apoptosis : an international journal on programmed cell death · 2026Article
- IGF2-associated tumor cells and APOE-positive macrophages define an imatinib resistance-associated niche in gastrointestinal stromal tumors.Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association · 2026Article
- From Glycan Biology to Drug Candidates: An Integrated Sialylation Niche Index and AI-Guided Therapeutic Framework for Head and Neck Squamous Cell Carcinoma.Biomedicines · 2026Article
- Cross-Cohort Integration of Blood DNA Methylation and Sepsis Transcriptomes Prioritizes TP53INP1 as a Candidate Associated with B-Cell Transcriptomic Patterns in Pediatric HAdV-7-Associated Sepsis.Pathogens (Basel, Switzerland) · 2026Article
- Multi-Omics Genome-Wide to Explore the Formation and Development Targets for Intracranial Aneurysms.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2026Article
- Integrative Transcriptomic Profiling Delineates LTBP4-Driven Fibroblast Reprogramming Across the Ossification Continuum of the Ligamentum Flavum.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2026Article
- Multiscale Transcriptomic and Molecular Modeling Analyses Suggest DCPMU-Associated Epithelial Remodeling and Tumor Microenvironment Perturbation in Prostate Cancer.Current issues in molecular biology · 2026Article
- Age-related IGF-1 decline permits a redox-sensitive transcriptional shift that directs hematopoiesis toward a CCR2Redox biology · 2026Article
- SOCS2 Downregulation Is Associated with a Ferro-Aging-Related Transcriptomic Signature in Proximal Tubular Cells in Chronic Kidney Disease.Biomedicines · 2026Article
- Ferroptosis Signatures in Diabetic Cardiomyopathy: Multi-Omics Discovery and Validation of ACOT1 and TXNIP.Current issues in molecular biology · 2026Article
- Identifying the therapeutic effects of talniflumate in metastatic papillary thyroid microcarcinoma through integrating multiple omics analysis.Naunyn-Schmiedeberg's archives of pharmacology · 2026Article
157 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors.
Funding
Abstract
Gene knockout (KO) experiments are a proven, powerful approach for studying gene function. However, systematic KO experiments targeting a large number of genes are usually prohibitive due to the limit of experimental and animal resources. Here, we present scTenifoldKnk, an efficient virtual KO tool that enables systematic KO investigation of gene function using data from single-cell RNA sequencing (scRNA-seq). In scTenifoldKnk analysis, a gene regulatory network (GRN) is first constructed from scRNA-seq data of wild-type samples, and a target gene is then virtually deleted from the constructed GRN. Manifold alignment is used to align the resulting reduced GRN to the original GRN to identify differentially regulated genes, which are used to infer target gene functions in analyzed cells. We demonstrate that the scTenifoldKnk-based virtual KO analysis recapitulates the main findings of real-animal KO experiments and recovers the expected functions of genes in relevant cell types.
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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.