Document Type
Conference Proceeding
Publication Date
2019
Publisher
Association for Computing Machinery
Source Publication
Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics
Source ISSN
978-1-4503-6666-3
Abstract
Uncovering genotype-phenotype relationships is a fundamental challenge in genomics. Gene prioritization is an important step for this endeavor to make a short manageable list from a list of thousands of genes coming from high-throughput studies. Network propagation methods are promising and state of the art methods for gene prioritization based on the premise that functionally-related genes tend to be close to each other in the biological networks.
In this study, we present PhenoGeneRanker, an improved version of a recently developed network propagation method called Random Walk with Restart on Multiplex Heterogeneous Networks (RWR-MH). PhenoGeneRanker allows multi-layer gene and disease networks. It also calculates empirical p-values of gene ranking using random stratified sampling of genes based on their connectivity degree in the network.
We ran PhenoGeneRanker using multi-omics datasets of rice to effectively prioritize the cold tolerance-related genes. We observed that top genes selected by PhenoGeneRanker were enriched in cold tolerance-related Gene Ontology (GO) terms whereas bottom ranked genes were enriched in general GO terms only. We also observed that top-ranked genes exhibited significant p-values suggesting that their rankings were independent of their degree in the network.
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.
Recommended Citation
Dursun, Cagatay; Shimoyama, Naoki; Shimoyama, Mary; Schläppi, Michael; and Bozdag, Serdar, "PhenoGeneRanker: A Tool for Gene Prioritization Using Complete Multiplex Heterogeneous Networks" (2019). Computer Science Faculty Research and Publications. 22.
https://epublications.marquette.edu/comp_fac/22
ADA Accessible Version
Included in
Biology Commons, Biotechnology Commons, Computer Sciences Commons
Comments
Published in Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, 2019: 279-288. DOI. The copyright holder for this preprint is the author/funder. It is made available under a CC-BY 4.0 International license. Used with permission.