Figure 7. Interaction with self-peptides in the selection of shared and unshared sequences.

Fold changes (mean ± SEM) in the relative aa frequencies versus hydrophobicity of the aa based on Gibbs free energy at P6 (A) or P7 (B) for transition from DP-CD69^– to DP-CD69⁺ cells and from there to SP cell subsets in experiment 2, and also in transition from SP-CD8 and SP-CD4 to peripheral CD8⁺ and CD4⁺ cells for experiment 3. Spearman’s correlation coefficient R and P values from the nonparametric Spearman’s correlation test are shown. Negative R values imply that, as hydrophobicity increases, so does the fold change in the relative aa frequency across the 2 cell populations. *P < 0.05, **P < 0.01, and ***P < 0.001, by unpaired t test. (C) Differential abundance of each aa at each position in CDR3β, computed by random selection of a length-matched unshared sequence for each shared sequence. Shared sequences are those present in at least 2 mice, and unshared sequences are unique to a single mouse. Only results for aa producing a Benjamini-Hochberg–adjusted P value of less than 0.05 by Fisher’s exact test are shown. The aa plotted at a frequency of 0 were preferentially used at that position in shared sequences, whereas those with a frequency of less than 0 were preferentially used in unshared sequences.