GAIL: An interactive webserver for inference and dynamic visualization of gene-gene associations based on gene ontology guided mining of biomedical literature

Couch, Daniel; Yu, Zhenning; Nam, Jin Hyun; Allen, Carter; Ramos, Paula S.; da Silveira, Willian A.; Hunt, Kelly J.; Hazard, Edward S.; Hardiman, Gary; Lawson, Andrew; Chung, Dongjun

Abstract

In systems biology, inference of functional associations among genes is compelling because the construction of functional association networks facilitates biomarker discovery. Specifically, such gene associations in human can help identify putative biomarkers that can be used as diagnostic tools in treating patients. Although biomedical literature is considered a valuable data source for this task, currently only a limited number of webservers are available for mining gene-gene associations from the vast amount of biomedical literature using text mining techniques. Moreover, these webservers often have limited coverage of biomedical literature and also lack efficient and user-friendly tools to interpret and visualize mined relationships among genes. To address these limitations, we developed GAIL (Gene-gene Association Inference based on biomedical Literature), an interactive webserver that infers human gene-gene associations from Gene Ontology (GO) guided biomedical literature mining and provides dynamic visualization of the resulting association networks and various gene set enrichment analysis tools. We evaluate the utility and performance of GAIL with applications to gene signatures associated with systemic lupus erythematosus and breast cancer. Results show that GAIL allows effective interrogation and visualization of gene-gene networks and their subnetworks, which facilitates biological understanding of gene-gene associations. GAIL is available at http://chunglab.io/GAIL/.

Citation

Couch, D., Yu, Z., Nam, J. H., Allen, C., Ramos, P. S., da Silveira, W. A., …Chung, D. (2019). GAIL: An interactive webserver for inference and dynamic visualization of gene-gene associations based on gene ontology guided mining of biomedical literature. PLoS ONE, 14(7), Article e0219195. https://doi.org/10.1371/journal.pone.0219195

• Journal Article Type: Article
• Acceptance Date: Jun 18, 2019
• Online Publication Date: Jul 1, 2019
• Publication Date: Jul 1, 2019
• Deposit Date: Oct 25, 2024
• Publicly Available Date: Oct 25, 2024
• Journal: PLOS ONE
• Publisher: Public Library of Science
• Peer Reviewed: Peer Reviewed
• Volume: 14
• Issue: 7
• Article Number: e0219195
• DOI: https://doi.org/10.1371/journal.pone.0219195