Deep-AGP: Prediction of angiogenic protein by integrating two-dimensional convolutional neural network with discrete cosine transform

Angiogenic proteins (AGPs) play a primary role in the formation of new blood vessels from pre-existing ones. AGPs have diverse applications in cancer, including serving as biomarkers, guiding anti-angiogenic therapies, and aiding in tumor imaging. Understanding the role of AGPs in cardiovascular and neurodegenerative diseases is vital for developing new diagnostic tools and therapeutic approaches. Considering the significance of AGPs, in this research, we first time established a computational model using deep learning for identifying AGPs. First, we constructed a sequence-based dataset. Second, we explored features by designing a novel feature encoder, called position-specific scoring matrix-decomposition-discrete cosine transform (PSSM-DC-DCT) and existing descriptors including Dipeptide Deviation from Expected Mean (DDE) and bigram-position-specific scoring matrix (Bi-PSSM). Third, each feature set is fed into two-dimensional convolutional neural network (2D-CNN) and machine learning classifiers. Finally, the performance of each learning model is validated by 10-fold cross-validation (CV). The experimental results demonstrate that 2D-CNN with proposed novel feature descriptor achieved the highest success rate on both training and testing datasets. In addition to being an accurate predictor for identification of angiogenic proteins, our proposed method (Deep-AGP) might be fruitful in understanding cancer, cardiovascular, and neurodegenerative diseases, development of their novel therapeutic methods and drug designing.