Charoenkwan P.Pipattanaboon C.Nantasenamat C.Hasan M.M.Moni M.A.Lio P.Shoombuatong W.Mahidol University2023-05-192023-05-192023-01-01Computers in Biology and Medicine Vol.152 (2023)00104825https://repository.li.mahidol.ac.th/handle/20.500.14594/81804Despite the arsenal of existing cancer therapies, the ongoing recurrence and new cases of cancer pose a serious health concern that necessitates the development of new and effective treatments. Cancer immunotherapy, which uses the body's immune system to combat cancer, is a promising treatment option. As a result, in silico methods for identifying and characterizing tumor T cell antigens (TTCAs) would be useful for better understanding their functional mechanisms. Although few computational methods for TTCA identification have been developed, their lack of model interpretability is a major drawback. Thus, developing computational methods for the effective identification and characterization of TTCAs is a critical endeavor. PSRTTCA, a new machine learning (ML)-based approach for improving the identification and characterization of TTCAs based on their primary sequences, is proposed in this study. Specifically, we introduce a new propensity score representation learning algorithm that allows one to generate various sets of propensity scores of amino acids, dipeptides, and g-gap dipeptides to be TTCAs. To enhance the predictive performance, optimal sets of variant propensity scores were determined and fed into the final meta-predictor (PSRTTCA). Benchmarking results revealed that PSRTTCA was a more precise and promising tool for the identification and characterization of TTCAs than conventional ML classifiers and existing methods. Furthermore, PSR-derived propensities of amino acids in becoming TTCAs are used to reveal the relationship between TTCAs and their informative physicochemical properties in order to provide insights into TTCA characteristics. Finally, a user-friendly online computational platform of PSRTTCA is publicly available at http://pmlabstack.pythonanywhere.com/PSRTTCA. The PSRTTCA predictor is anticipated to facilitate community-wide efforts in accelerating the discovery of novel TTCAs for cancer immunotherapy and other clinical applications.Computer ScienceArticleSCOPUS10.1016/j.compbiomed.2022.1063682-s2.0-851438419931879053436481763