iTTCA-MFF: identifying tumor T cell antigens based on multiple feature fusion.

Hongliang Zou, Fan Yang, Zhijian Yin

Immunogenetics 2022 Oct

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Cancer is a terrible disease, recent studies reported that tumor T cell antigens (TTCAs) may play a promising role in cancer treatment. Since experimental methods are still expensive and time-consuming, it is highly desirable to develop automatic computational methods to identify tumor T cell antigens from the huge amount of natural and synthetic peptides. Hence, in this study, a novel computational model called iTTCA-MFF was proposed to identify TTCAs. In order to describe the sequence effectively, the physicochemical (PC) properties of amino acid and residue pairwise energy content matrix (RECM) were firstly employed to encode peptide sequences. Then, two different approaches including covariance and Pearson's correlation coefficient (PCC) were used to collect discriminative information from PC and RECM matrixes. Next, an effective feature selection approach called the least absolute shrinkage and selection operator (LAASO) was adopted to select the optimal features. These selected optimal features were fed into support vector machine (SVM) for identifying TTCAs. We performed experiments on two different datasets, experimental results indicated that the proposed method is promising and may play a complementary role to the existing methods for identifying TTCAs. The datasets and codes can be available at https://figshare.com/articles/online_resource/iTTCA-MFF/17636120 . © 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.

Citation

Hongliang Zou, Fan Yang, Zhijian Yin. iTTCA-MFF: identifying tumor T cell antigens based on multiple feature fusion. Immunogenetics. 2022 Oct;74(5):447-454