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bioRxiv · 10.1101/651000

PhenoGeneRanker: A Tool for Gene Prioritization Using Complete Multiplex Heterogeneous Networks

Dursun, C.·Shimoyama, N.·Shimoyama, M.·Schlappi, M.·Bozdag, S.
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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.\n\nIn 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.\n\nWe 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.\n\nCCS CONCEPTS* Bioinformatics * Biological networks * System biology * Computational genomics\n\nAvailability and implementationThe source code is available on GitHub at https://github.com/bozdaglab/PhenoGeneRanker under Creative Commons Attribution 4.0 license\n\nContactcdursun@mcw.edu or serdar.bozdag@marquette.edu

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Dursun, C., Shimoyama, N., Shimoyama, M., Schlappi, M., Bozdag, S.. 2019-05-27. PhenoGeneRanker: A Tool for Gene Prioritization Using Complete Multiplex Heterogeneous Networks. https://doi.org/10.1101/651000

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