Analyzing a co-occurrence gene-interaction network to identify disease-gene association

• Main Authors: Amira Al-Aamri, Kamal Taha, Yousof Al-Hammadi, Maher Maalouf, Dirar Homouz
• Format: Article
• Language: English
• Published: BMC 2019-02-01
• Series: BMC Bioinformatics
• Subjects: Text mining; Disease-gene association; Biological NLP; Biomedical literature; Genetic network
• Online Access: http://link.springer.com/article/10.1186/s12859-019-2634-7

Abstract Background Understanding the genetic networks and their role in chronic diseases (e.g., cancer) is one of the important objectives of biological researchers. In this work, we present a text mining system that constructs a gene-gene-interaction network for the entire human genome and then performs network analysis to identify disease-related genes. We recognize the interacting genes based on their co-occurrence frequency within the biomedical literature and by employing linear and non-linear rare-event classification models. We analyze the constructed network of genes by using different network centrality measures to decide on the importance of each gene. Specifically, we apply betweenness, closeness, eigenvector, and degree centrality metrics to rank the central genes of the network and to identify possible cancer-related genes. Results We evaluated the top 15 ranked genes for different cancer types (i.e., Prostate, Breast, and Lung Cancer). The average precisions for identifying breast, prostate, and lung cancer genes vary between 80-100%. On a prostate case study, the system predicted an average of 80% prostate-related genes. Conclusions The results show that our system has the potential for improving the prediction accuracy of identifying gene-gene interaction and disease-gene associations. We also conduct a prostate cancer case study by using the threshold property in logistic regression, and we compare our approach with some of the state-of-the-art methods.