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PhenoMetaboDiff: R Package for Analysis and Visualization of Phenotype Microarray Data
Rini Pauly1,2, Mehtab Iqbal3, Narae Lee2
1JC Self Research Institute, 106 Gregor Mendel Circle, Greenwood, SC 29646, USA.
Background:
PhenoMetaboDiff is a novel R package for computational analysis and visualization of data generated by Biolog Phenotype Mammalian Microarrays (PM-Ms). These arrays measure the energy production of mammalian cells in different metabolic environments, assess the metabolic activity of cells exposed to various drugs or energy sources, and compare the metabolic profiles of cells from individuals affected by specific disorders versus healthy controls.
Methods:
PhenoMetaboDiff has several modules that facilitate statistical analysis by sample comparisons using non-parametric Mann-Whitney U-test, the integration of the OPM package (an R package for analysing OmniLog® phenotype microarray data) for robust file conversion, and calculation of slope and area under the curve (AUC). In addition, the built-in visualization allows specific wells to be visualized in selected pathways for a particular time slice.
Results:
Compared to the standard OPM package, the features developed in PhenoMetaboDiff assess metabolic profiles by employing statistical tests and visualize the dynamic nature of the energy production in several conditions. Examples of how this package can be used are demonstrated for several rare disease conditions. The incorporation of a graphical user interface expands the utility of this program to both expert and novice users of R.
Conclusions:
PhenoMetaboDiff makes the deployment of the cutting-edge Biolog system available to any researcher.
