An In-silico Study for Available Microarray Datasets Analysis for Tropheryma whipplei to Evaluate Impact of Drug and Thermic Stress
Author(s): Amit Joshi and Vikas Kaushik*
Abstract
Tropheryma whipplei is a Gram-positive rod-shaped bacteria, a member of the Actinobacteria division that causes Whipple’s disease. This disease is very harmful as it can cause multiple organ failure including lipodystrophy of intestine and central nervous system functionality. Therefore this study was found crucial for identification of genes that are affected within T. whipplei due to temperature and commonly used drug Doxycycline. This will assist in future drug repurposing against the bacterium. The Gene expression profiling analysis was performed using GEO2R that compares two or more groups of samples in order to identify genes that are differentially expressed across experimental conditions. Force normalization which uses quantile normalization was applied for the array normalization to the expression data making all selected samples have identical value distribution. Limma package was used for the p value calculation between different groups. The study on the series GSE5717 shows that higher doses of Doxycycline drug treatments on the bacterium T. whipplei does not have much impact, as bacterium survival strategies also enhances both directly and indirectly. Therefore, the search for new drug or novel vaccine candidate research by in-silico mode is required for rapid development of treatment. While analyzing the series GSE3693, it was found that thermic stress on bacterium can activate bacterium survival genetic makeup. Our findings suggest that T. whipplei has a distinct adaptive control to thermal stressors, which is consistent with its presumed environment origins. Also, it was found that higher concentration of Doxycycline, up-regulation of membrane proteins like ATP Binding cassette transporters, which may create export and detoxify systems by which T. whipplei may restrict the impact of the bactericidal chemical.
