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. 2024 Nov 15;44(1):1–29. doi: 10.1038/s44318-024-00298-9

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© The Author(s) 2024

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. Creative Commons Public Domain Dedication waiver http://creativecommons.org/publicdomain/zero/1.0/ applies to the data associated with this article, unless otherwise stated in a credit line to the data, but does not extend to the graphical or creative elements of illustrations, charts, or figures. This waiver removes legal barriers to the re-use and mining of research data. According to standard scholarly practice, it is recommended to provide appropriate citation and attribution whenever technically possible.

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(A) UMAP projection of 22,595 epithelial cells from oropharyngeal squamous cell carcinoma samples (n = 10; 18,619 malignant cells (red), 695 non-malignant cells (purple)), and matched normal tonsil (n = 7; 3281 cells (blue)). (B) GOBP terms enriched amongst the sets of 100 genes that were co-expressed with either APOBEC3A or APOBEC3B in 2649 (after QC) epithelial cells from normal tonsil. Terms ranked by P value calculated by EnrichR package (Fisher Exact test bias corrected using the z-score of the deviation from the expected rank). (C) UMAP projection depicting four phenotypes (basal, proliferating, differentiating, terminally differentiated) displayed by the normal tonsillar epithelial cells in our dataset. (D) Marker genes are used to identify the four epithelial phenotypes represented in (C). (E) Violin plots of gene expression in individual tonsillar epithelial cells, and UMAP projections of the density of gene expression in the tonsillar epithelial subtypes. (****P < 0.0001, Wilcoxon’s rank-sum test; Basal, n = 1047; Proliferating, n = 353; Differentiating, n = 1091; Terminally differentiated, n = 158).