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. 2023 May 19;29(5):1273–1286. doi: 10.1038/s41591-023-02324-5

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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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 2 — a, Correlation between immune gene signatures and TCR metrics from immunoSEQ DNA sequencing. b, Scatter-plots visualizing correlation between ICR score, productive TCR clonality by immunoSEQ DNA sequencing and TCR clonality as determined by MiXCR using RNA-seq data. Pearson’s r and P value of the correlations are indicated. The gray area reflects the 95% confidence level interval for predictions of the linear regression model. c, Visualization of a T cell repertoire with a high clonality (top) and low clonality (bottom). Each color represents a unique T cell clone, proportions are represented as illustrative circle diagrams. Violin plots show the relationship between productive TCR clonality and ICR classification and CMS subtypes, center line, box limits and whiskers represent the median, interquartile range and 1.5× interquartile range. P values were calculated using a two-sided, unpaired Student’s t-test. d, Pearson correlation between all genes (n = 18,270) and TCR clonality (colored, FDR < 0.05). Top ten genes with highest positive correlation and top ten genes with highest inverse correlation are labeled. FDR calculated by Benjamini–Hochberg correction. e, Core network of genes with the highest association with productive TCR clonality (top 50 genes) using Ingenuity Pathway Analysis. f,g, Pearson’s correlation between immunoSEQ-based TCR productive clonality and the expression of ICR genes (f) and genes that express markers of tumor-reactive CD8⁺ T cells (g). The magnitude of significance for each correlation is represented by the number in the green square indicating the exponent (x) in the scientific notation of the FDR (x10^-x). h, Example scatter-plots for an ICR-high sample and an ICR-low sample showing overlap between clones from the primary tumor and its matching healthy colon tissue sample. Tumor-enriched T cell clones (>0.1% in the tumor, which are at least 32 times higher in the tumor compared to normal) are highlighted. i, Correlation of proportion of tumor-enriched T cell clones in the tumor (in percent) with ICR score. Pearson’s r and P value of the correlation are indicated in the plot. All P values are two-sided.