Figure 4:

Breast cancer results. (a) Classification accuracy obtained by patient-holdout cross-validation, where the tumor and healthy tissue from the same patient are excluded for validation. (b) Illustration of the classifier weights after fitting the model to all 16 patients. For each of the five Atchley factors, the weights are shown for the four residue positions. The weight for the log-frequency of the receptor is also shown. Positive weight values are shown pointing up, and negative weight values are shown pointing down. The length of the arrow corresponds to the weight’s magnitude. (c) All 4-mers with a score above 0.5 (middle column) shown for each of the 16 patients (leftmost column). Each 4-mer is shown in the context of its respective CDR3. When the 4-mer appears in multiple CDR3 sequences, the CDR3 with the largest relative abundance is shown. The CDR3 sequences are ranked according to their relative abundance in the sample (rightmost column). A rank of 1 indicates the largest relative abundance in the sample. As with colorectal cancer, we observed TCRβ CDR3 sequences containing multiple high-scoring 4-mers. In patient 1, LSRS and RSNQ appear in the TCRβ CDR3 sequence CASSLSRSNQPQHF. In patient 10, SSPH, AYNQ, and AAYN appear in the TCRβ CDR3 sequence CASSSPHRAAYNQPQHF.