AuthorsAlanis Lobato, Gregorio
Cannistraci, Carlo Vittorio
KAUST DepartmentBiological and Environmental Sciences and Engineering (BESE) Division
Computational Bioscience Research Center (CBRC)
Computer Science Program
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Integrative Systems Biology Lab
Online Publication Date2015-01-30
Print Publication Date2015-07
Permanent link to this recordhttp://hdl.handle.net/10754/344117
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AbstractDetecting structure in population genetics and case-control studies is important, as it exposes phenomena such as ecoclines, admixture and stratification. Principal Component Analysis (PCA) is a linear dimension-reduction technique commonly used for this purpose, but it struggles to reveal complex, nonlinear data patterns. In this paper we introduce non-centred Minimum Curvilinear Embedding (ncMCE), a nonlinear method to overcome this problem. Our analyses show that ncMCE can separate individuals into ethnic groups in cases in which PCA fails to reveal any clear structure. This increased discrimination power arises from ncMCE's ability to better capture the phylogenetic signal in the samples, whereas PCA better reflects their geographic relation. We also demonstrate how ncMCE can discover interesting patterns, even when the data has been poorly pre-processed. The juxtaposition of PCA and ncMCE visualisations provides a new standard of analysis with utility for discovering and validating significant linear/nonlinear complementary patterns in genetic data.
CitationAlanis-Lobato, G., Cannistraci, C. V., Eriksson, A., Manica, A., & Ravasi, T. (2015). Highlighting nonlinear patterns in population genetics datasets. Sci. Rep., 5. doi: 10.1038/srep08140
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