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BMC Proc. 2018 Sep 17;12(Suppl 9):59. doi: 10.1186/s12919-018-0122-0. eCollection 2018.

Identification of epistatic interactions between the human RNA demethylases FTO and ALKBH5 with gene set enrichment analysis informed by differential methylation.

Author information

1
Institute for Biomedical Informatics, Richards Medical Research Laboratories, Perelman School of Medicine, University of Pennsylvania, 3700 Hamilton Walk, Philadelphia, PA 19104 USA.

Abstract

The Genetic Analysis Workshop (GAW) presents an opportunity to collaboratively evaluate methodology relevant to current issues in genetic epidemiology. The GAW20 data combine real clinical trial data with fictitious epigenetic drug response endpoints. Considering the evidence suggesting that networks of interactions between many genes underlie complex phenotypes, we utilize differential methylation status to identify a relevant gene set for enrichment analysis and use this to infer potential biological function underlying drug response. We highlight the pertinence of considering the potential for widespread epistatic interactions in the absence of main effects, and present evidence of epistasis between single-nucleotide polymorphisms (SNPs) on the two RNA demethylases FTO and ALKBH5.

Conflict of interest statement

Not applicable.Not applicable.The authors declare that they have no competing interests.Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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