In the omic era, one of the main aims is to discover groups of functionally related genes that drive the difference between different conditions. To this end, a plethora of potentially useful multivariate statistical approaches has been proposed, but their evaluation is hindered by the absence of a gold standard. Here, we propose a method for simulating biological data-gene expression, RPKM/FPKM or protein abundances-from two conditions, namely, a reference condition and a perturbation of it. Our approach is built upon probabilistic graphical models and is thus especially suited for testing topological wapproaches.
SALVIATO, E., DJORDJILOVIC, V., CHIOGNA, M., ROMUALDI, C. (2017). simPATHy: a new method for simulating data from perturbed biological PATHways. BIOINFORMATICS, 33(3), 456-457 [10.1093/bioinformatics/btw642].
simPATHy: a new method for simulating data from perturbed biological PATHways
CHIOGNA, MONICA;
2017
Abstract
In the omic era, one of the main aims is to discover groups of functionally related genes that drive the difference between different conditions. To this end, a plethora of potentially useful multivariate statistical approaches has been proposed, but their evaluation is hindered by the absence of a gold standard. Here, we propose a method for simulating biological data-gene expression, RPKM/FPKM or protein abundances-from two conditions, namely, a reference condition and a perturbation of it. Our approach is built upon probabilistic graphical models and is thus especially suited for testing topological wapproaches.File | Dimensione | Formato | |
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