Predicting Algorithm of Tissue Cell Ratio Based on Deep Learning Using Single-Cell RNA Sequencing

Abstract

Background: Understanding the proportion of cell types in heterogeneous tissue samples is important in bioinformatics. It is a challenge to infer the proportion of tissues using bulk RNA sequencing data in bioinformatics because most traditional algorithms for predicting tissue cell ratios heavily rely on standardized specific cell-type gene expression profiles, and do not consider tissue heterogeneity. The prediction accuracy of algorithms is limited, and robustness is lacking. This means that new approaches are needed urgently. Methods: In this study, we introduced an algorithm that automatically predicts tissue cell ratios named Autoptcr. The algorithm uses the data simulated by single-cell RNA sequencing (ScRNA-Seq) for model training, using convolutional neural networks (CNNs) to extract intrinsic relationships between genes and predict the cell proportions of tissues. Results: We trained the algorithm using simulated bulk samples and made predictions using real bulk PBMC data. Comparing Autoptcr with existing advanced algorithms, the Pearson correlation coefficient between the actual value of Autoptcr and the predicted value was the highest, reaching 0.903. Tested on a bulk sample, the correlation coefficient of Lin was 41% higher than that of CSx. The algorithm can infer tissue cell proportions directly from tissue gene expression data. Conclusions: The Autoptcr algorithm uses simulated ScRNA-Seq data for training to solve the problem of specific cell-type gene expression profiles. It also has high prediction accuracy and strong noise resistance for the tissue cell ratio. This work is expected to provide new research ideas for the prediction of tissue cell proportions.