Fig. 6: Characteristics of complementary determining region 3 (CDR3) length, hydrophobicity, motifs, and V-J gene combinations in expanded and contracted T-cell receptor (TCR) clones.
From: T-cell receptor clonotypic diversity and specialization in digestive system cancers
A Density plot showing the distribution of CDR3 lengths in expanded, contracted, and stable clones. B Bar plot showing amino acid usage frequency in expanded and contracted clones. Differences were evaluated using the two-sided t-test. C Density plot showing the distribution of CDR3 hydrophobicity in expanded and contracted clones. Differences were assessed using the Kolmogorov–Smirnov (ks) test. D SeqLogo showing the conserved motif distributions in expanded and contracted clones. E Bar plot highlighting the top 11 motifs in expanded clones with the highest log2 fold changes compared to contracted clones. F Bar plot showing the distribution of clones containing the NYGYTF motif, identified as the motif with the highest enrichment ratio. G Density plot showing the positional distribution of the NYGYTF motif within the CDR3 region of expanded and contracted clones. Differences were assessed using the Kolmogorov–Smirnov (ks) test. H Bar plot displaying the top 20 V − J gene combinations in clones containing the NYGYTF motif. I Kaplan–Meier survival curves showing the association between selected V − J gene activity scores and patient prognosis. P values were calculated using the log-rank test. J Sankey plot illustrating the flow from antigen genes (antigen.gene) to epitopes (antigen.epitope), major histocompatibility complex (MHC) alleles (mhc.a), and TCR V − J pairs in colorectal cancer (CRC), based on high-confidence Homo sapiens data from VDJdb28. Flow widths represent frequencies; data were filtered for specific V − J pairs. K Kaplan–Meier survival plot showing the association between MLANA expression and patient prognosis in the TCGA-COAD cohort. P value was calculated using the log-rank test. L Box plot showing the distribution of MLANA expression in tumor and normal samples from the “The Cancer Genome Atlas Colorectal Adenocarcinoma” (TCGA-COAD) cohort. (M) Violin plot showing the distribution of MLANA expression in tumor and normal samples from the GSE110224 cohort36. P value was obtained using the two-sided t-test.
