ArticleJournal of immunology (Baltimore, Md. : 1950)2016
Categorical Analysis of Human T Cell Heterogeneity with One-Dimensional Soli-Expression by Nonlinear Stochastic Embedding.
Article in Journal of immunology (Baltimore, Md. : 1950), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
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- SUMOylation inhibitors activate anti-tumor immunity by reshaping the immune microenvironment in a preclinical model of hepatocellular carcinoma.Cellular oncology (Dordrecht, Netherlands) · 2024Article
- Single-cell atlas reveals characteristic changes in intrahepatic HBV-specific leukocytes.Microbiology spectrum · 2024Article
- Single-cell mass cytometry in immunological skin diseases.Frontiers in immunology · 2024Review
- Review
- 2,5-dimethylcelecoxib alleviated NK and T-cell exhaustion in hepatocellular carcinoma via the gastrointestinal microbiota-AMPK-mTOR axis.Journal for immunotherapy of cancer · 2023Article
- Piecewise differentiation of the fractional order CAR-T cells-SARS-2 virus model.Results in physics · 2022Article
- PRI: Re-Analysis of a Public Mass Cytometry Dataset Reveals Patterns of Effective Tumor Treatments.Frontiers in immunology · 2022Article
- Acquisition of murine splenic myeloid cells for protein and gene expression profiling by advanced flow cytometry and CITE-seq.STAR protocols · 2021Article
- A Targeted Multi-omic Analysis Approach Measures Protein Expression and Low-Abundance Transcripts on the Single-Cell Level.Cell reports · 2020Article
- Single-Cell Approaches to Profile the Response to Immune Checkpoint Inhibitors.Frontiers in immunology · 2020Review
- Key steps and methods in the experimental design and data analysis of highly multi-parametric flow and mass cytometry.Computational and structural biotechnology journal · 2020Review
- Exploring genetic interaction manifolds constructed from rich single-cell phenotypes.Science (New York, N.Y.) · 2019Article
- Fast interpolation-based t-SNE for improved visualization of single-cell RNA-seq data.Nature methods · 2019Article
- Use of Mass Cytometry to Profile Human T Cell Exhaustion.Frontiers in immunology · 2019Review
- Mixed-effects association of single cells identifies an expanded effector CD4Science translational medicine · 2018Article
- CAR T cells for infection, autoimmunity and allotransplantation.Nature reviews. Immunology · 2018Review
- TNature reviews. Immunology · 2018Review
- Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Rapid progress in single-cell analysis methods allow for exploration of cellular diversity at unprecedented depth and throughput. Visualizing and understanding these large, high-dimensional datasets poses a major analytical challenge. Mass cytometry allows for simultaneous measurement of >40 different proteins, permitting in-depth analysis of multiple aspects of cellular diversity. In this article, we present one-dimensional soli-expression by nonlinear stochastic embedding (One-SENSE), a dimensionality reduction method based on the t-distributed stochastic neighbor embedding (t-SNE) algorithm, for categorical analysis of mass cytometry data. With One-SENSE, measured parameters are grouped into predefined categories, and cells are projected onto a space composed of one dimension for each category. In contrast with higher-dimensional t-SNE, each dimension (plot axis) in One-SENSE has biological meaning that can be easily annotated with binned heat plots. We applied One-SENSE to probe relationships between categories of human T cell phenotypes and observed previously unappreciated cellular populations within an orchestrated view of immune cell diversity. The presentation of high-dimensional cytometric data using One-SENSE showed a significant improvement in distinguished T cell diversity compared with the original t-SNE algorithm and could be useful for any high-dimensional dataset.
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