Detecting gene–gene interactions from GWAS using diffusion kernel principal components

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dc.contributor.authorWalakira, Andrew
dc.contributor.authorOcira, Junior
dc.contributor.authorDuroux, Diane
dc.contributor.authorFouladi, Ramouna
dc.contributor.authorMoškon, Miha
dc.contributor.authorRozman, Damjana
dc.contributor.authorSteen, Kristel Van
dc.date.accessioned2023-05-08T17:19:10Z
dc.date.available2023-05-08T17:19:10Z
dc.date.issued2022
dc.description.abstractGenes and gene products do not function in isolation but as components of complex networks of macromolecules through physical or biochemical interactions. Dependencies of gene mutations on genetic background (i.e., epistasis) are believed to play a role in understanding molecular underpinnings of complex diseases such as inflammatory bowel disease (IBD). However, the process of identifying such interactions is complex due to for instance the curse of high dimensionality, dependencies in the data and non-linearity. Here, we propose a novel approach for robust and computationally efficient epistasis detection. We do so by first reducing dimensionality, per gene via diffusion kernel principal components (kpc). Subsequently, kpc gene summaries are used for downstream analysis including the construction of a gene-based epistasis network. We show that our approach is not only able to recover known IBD associated genes but also additional genes of interest linked to this difficult gastrointestinal disease.en_US
dc.identifier.citationWalakira, A., Ocira, J., Duroux, D., Fouladi, R., Moškon, M., Rozman, D., & Van Steen, K. (2022). Detecting gene–gene interactions from GWAS using diffusion kernel principal components. Bmc Bioinformatics, 23(1), 1-18. https://doi.org/10.1186/s12859-022-04580-7en_US
dc.identifier.urihttps://doi.org/10.1186/s12859-022-04580-7
dc.identifier.urihttps://nru.uncst.go.ug/handle/123456789/8655
dc.language.isoenen_US
dc.publisherBmc Bioinformaticsen_US
dc.subjectInflammatory bowel diseaseen_US
dc.subjectDiffusion kernel principal componentsen_US
dc.subjectBivariate synergyen_US
dc.subjectSpike and slab priorsen_US
dc.subjectGene epistasis networken_US
dc.titleDetecting gene–gene interactions from GWAS using diffusion kernel principal componentsen_US
dc.typeArticleen_US
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