ArticleBMC genomics2014
Visualisation of the T cell differentiation programme by Canonical Correspondence Analysis of transcriptomes.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Machine learning-assisted decoding of temporal transcriptional dynamics via fluorescent timer.Nature communications · 2025Article
- A multidimensional toolkit for elucidating temporal trajectories in cell development in vivo.Development (Cambridge, England) · 2024Article
- Alterations of lung microbiota in lung transplant recipients with pneumocystis jirovecii pneumonia.Respiratory research · 2024Observational
- Unraveling T-cell dynamics using fluorescent timer: Insights from the Tocky system.Biophysics and physicobiology · 2024Review
- Spectrum of Treg and self-reactive T cells: single cell perspectives from old friend HTLV-1.Discovery immunology · 2024Review
- Nonlinear canonical correspondence analysis and its application.Scientific reports · 2023Article
- The pioneer transcription factors Foxa1 and Foxa2 regulate alternative RNA splicing during thymocyte positive selection.Development (Cambridge, England) · 2021Article
- From stability to dynamics: understanding molecular mechanisms of regulatory T cells through Foxp3 transcriptional dynamics.Clinical and experimental immunology · 2019Review
- Sonic Hedgehog Is a Determinant of γδ T-Cell Differentiation in the Thymus.Frontiers in immunology · 2019Article
- A timer for analyzing temporally dynamic changes in transcription during differentiation in vivo.The Journal of cell biology · 2018Article
- Gli3 in fetal thymic epithelial cells promotes thymocyte positive selection and differentiation by repression ofDevelopment (Cambridge, England) · 2018Article
- Elucidating T Cell Activation-Dependent Mechanisms for Bifurcation of Regulatory and Effector T Cell Differentiation by Multidimensional and Single-Cell Analysis.Frontiers in immunology · 2018Article
- Controversies concerning thymus-derived regulatory T cells: fundamental issues and a new perspective.Immunology and cell biology · 2016Article
- A genome wide transcriptional model of the complex response to pre-TCR signalling during thymocyte differentiation.Oncotarget · 2015Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
backgroundCurrently, in the era of post-genomics, immunology is facing a challenging problem to translate mutant phenotypes into gene functions based on high-throughput data, while taking into account the classifications and functions of immune cells, which requires new methods.
resultsHere we propose a novel application of a multidimensional analysis, Canonical Correspondence Analysis (CCA), to reveal the molecular characteristics of undefined cells in terms of cellular differentiation programmes by analysing two transcriptomic datasets. Using two independent datasets, whether RNA-seq or microarray data, CCA successfully visualised the cross-level relationships between genes, cells, and differentiation programmes, and thereby identified the immunological features of mutant cells (Gata3-KO T cells and Stat3-KO T cells) in a data-oriented manner. With a new concept, differentiation variable, CCA provides an automatic classification of cell samples, which had a high sensitivity and a comparable performance to other classification methods. In addition, we elaborate how CCA results can be interpreted, and reveal the features of CCA in comparison with other visualisation techniques.
conclusionsCCA is a visualisation tool with a classification ability to reveal the cross-level relationships of genes, cells and differentiation programmes. This can be used for characterising the functional defect of cells of interest (e.g. mutant cells) in the context of cellular differentiation. The proposed approach fits with common hypothesis-oriented studies in immunology, and can be used for a wide range of molecular and genomic studies on cellular differentiation mechanisms.
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