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. 2023 Oct 18;13:17714. doi: 10.1038/s41598-023-44693-4

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© The Author(s) 2023

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/.

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Gene expression and T cell receptor (TCR) features across single cell gene expression (GEX) defined clusters. (A) Selected genes and TCR features across the thymic GEX UMAP. Colour indicates expression of selected genes (top row) and Z-score normalised and GEX-neighbourhood averaged expression of the same genes (bottom row). Blue colour indicates negative values, red colour indicates positive values. (B) Differentially expressed genes across thymic GEX clusters. Dot colour indicates expression level, and dot size indicates the fraction of clonotypes expressing the gene. (C) Selected TCR features exhibiting variation across GEX clusters in a graph-versus-feature analysis. Numerical features indicating properties of the TCR repertoire are mapped onto a GEX cluster graph where clonotypes residing in the same GEX cluster are connected. Variation in the TCR features across the GEX cluster graph is assessed first by an initial t-test, then by a one-sided Mann–Whitney U test for the features with low t-test P values. Colours indicate direction of change (left) or adjusted Mann–Whitney U test P values (right).