An Ovarian Cancer Susceptible Gene Prediction Method Based on Deep Learning Methods

• Main Authors: Lu Ye, Yi Zhang, Xinying Yang, Fei Shen, Bo Xu
• Format: Article
• Language: English
• Published: Frontiers Media S.A. 2021-08-01
• Series: Frontiers in Cell and Developmental Biology
• Subjects: ovarian cancer; gene prediction; omics data; deep learning method; pathway analysis
• Online Access: https://www.frontiersin.org/articles/10.3389/fcell.2021.730475/full

Ovarian cancer (OC) is one of the most fatal diseases among women all around the world. It is highly lethal because it is usually diagnosed at an advanced stage which may reduce the survival rate greatly. Even though most of the patients are treated timely and effectively, the survival rate is still low due to the high recurrence rate of OC. With a large number of genome-wide association analysis (GWAS)-discovered risk regions of OC, expression quantitative trait locus (eQTL) analyses can explore candidate susceptible genes based on these risk loci. However, a large number of OC-related genes remain unknown. In this study, we proposed a novel gene prediction method based on different omics data and deep learning methods to identify OC causal genes. We first employed graph attention network (GAT) to obtain a compact gene feature representation, then a deep neural network (DNN) is utilized to predict OC-related genes. As a result, our model achieved a high AUC of 0.761 and AUPR of 0.788, which proved the accuracy and effectiveness of our proposed method. At last, we conducted a gene-set enrichment analysis to further explore the mechanism of OC. Finally, we predicted 245 novel OC causal genes and 10 top related KEGG pathways.