Fig. 5.

Alluvial diagram of the predicted TAAs for breast cancer based on TAPINTO parameters. The diagram visualizes the integration of various TAPINTO parameters and the resulting classification of gene candidates. The flow from left to right represents the algorithmic progression from individual parameter evaluation to final index scoring.(A) For the evaluation of TAAs, ERBB2 (also known as HER2), ESR1 (also known as ER), and 2 OR-encoding genes (OR11L1 and OR1G1) were considered positive control TAA antigens (HER2 and ER) and normal antigens. The P value, frequency (Freq), average expression (AvExp), and fold change (FC), which were calculated with TAPINTO, were used as criteria for TAA evaluation for the characterization of TAAs in the alluvial assay. The quantitative values were added as indexes to evaluate the TAA potential of the test object. (B) The TAPINTO parameters of other therapeutic TAA genes (CD274 and VEGFA) from clinical studies were also evaluated; ERBB2 and OR1G1 were again used as positive and negative controls, respectively. (C) Overall, 5,998 plasma-associated genes excluding the previous 6 genes were tested for their TAA potential. The 5,998 genes were evaluated from different perspectives based on the scale of the parameters and were classified from a score of 6 to 0. Among these, 5 genes (CXCL9, KCNJ3, SQLE, MMP11, and SLC7A2) achieved the highest score of 6 points, the same as ERBB2, and were identified as ideal TAA candidates. The flow direction of the plot is from left to right.