Combining gene ontology with deep neural networks to enhance the clustering of single cell RNA-Seq data

Background: Single cell RNA sequencing (scRNA-seq) is applied to assay the individual transcriptomes of large numbers of cells. The gene expression at single-cell level provides an opportunity for better understanding of cell function and new discoveries in biomedical areas. To ensure that the single-cell based gene expression data are interpreted appropriately, it is crucial to develop new computational methods. Results: In this article, we try to re-construct a neural network based on Gene Ontology (GO) for dimension reduction of scRNA-seq data. By integrating GO with both unsupervised and supervised models, two novel methods are proposed, named GOAE (Gene Ontology AutoEncoder) and GONN (Gene Ontology Neural Network) respectively. Conclusions: The evaluation results show that the proposed models outperform some state-of-the-art dimensionality reduction approaches. Furthermore, incorporating with GO, we provide an opportunity to interpret the underlying biological mechanism behind the neural network-based model.