Extended Data Fig. 2: Group 1 and 2 clonotypes differ in expansion and gene expression upon stimulation.
From: TCR sequencing paired with massively parallel 3′ RNA-seq reveals clonotypic T cell signatures
a, Clonal sizes of Group 1 and 2 clonotypes in the stimulated and ex vivo conditions shown in Fig. 3d. P value calculated by two-sample Mann-Whitney U test (Stimulated: n = 74 clonotype groups in Group 1; 37 Group 2 clonotypes. ex vivo: n = 82 Group 1 clonotypes; 40 Group 2 clonotypes). Box and whisker plots indicate the (box) 25th and 75th percentile along with (whisker) + /− 1.5*interquartile range. Violin plots represent estimated density of clonotypes. b, Gene expression fold changes between stimulated and ex vivo cells in (x-axis) Group 1 clonotypes and (y-axis) Group 2 clonotypes. Each point represents a shared gene across Group 1 and 2 clonotypes. Red line indicates fitted linear model. P value calculated by one-tailed F statistics (F(1,5908)) of the linear regression. n = 5908 genes. c, Volcano plots of differentially expressed genes between Group 1 and 2 clonotypes in the (left) stimulated and the (right) ex vivo conditions. P values were determined using a two-tailed likelihood ratio test, and adjusted by Bonferroni correction. Top 10 genes with positive or negative fold changes are labeled. Cells in Group 1 and 2 have been downsampled to 300 each (n = 300 cells for each of the groups). See Supplementary Table 13 for more details.
