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. 2017 Nov 6;214(11):3417–3433. doi: 10.1084/jem.20161784

Figure 5.

Figure 5.

PCA correlations among mice and humans for V and V–J usage. PCA shows the correlation between ABabDII mice (blue dots), ABabDR4 mice (red dots), and human donors (gray dots) for their TRAV usage (A) and TRBV usage (B) of unique TCR clonotypes. (Left) PCA of in-frame sequences; (right) PCA for out-of-frame sequences. TRAV1-1, TRAV1-2, TRBV5-1, and TRBV6-1 were excluded. Each dot represents an individual of ABabDII mice, ABabDR4 mice, or humans. Proportions of variance (PC1 and PC2) are indicated at the axis. (C) Comparisons of V segment usages restricted to the same or different MHC alleles. (Left) Similarity comparisons of out-of-frame V gene usages in ABabDII and ABabDR4. (Right, top and bottom lanes) Similarity comparisons of in frame V segment usages within and between groups of ABabDII mice, ABabDR4 mice, and humans and to the out-of-frame sequences. (Top) TCRα (TRAV) V segments; (bottom) TCRβ (TRBV) V segments. (D and E) PCA of TRAV-J (D) and TRBV-J (E) pairing usage of unique TCR clonotypes, arranged the same as in A and B. (F) Comparisons of V–J pairing usages restricted to the same or different MHC allele(s), arranged the same as in C. ***, P ≤ 0.001; **, 0.001 ≤ P < 0.05; and *, 0.05 ≤ P < 0.1; n.s., not significant (Mann–Whitney test, two-tailed). ED, Euclidean distance. Data are from ABabDII mice (n = 5), ABabDR4 mice (n = 5), and humans (n = 3). Fig. S4 provides PCA analysis of J segment usages.