S1: Percellome toxicogenomics data handling by Garuda
The Percellome Toxicogenomics Project is an initiative to collect gene expression profiles derived from mice that were exposed to various types of xenobiotics, aiming to reconstruct gene co-expression networks to investigate their toxicity. These microarray data were normalized by “Percellome” method [Kanno, J., et al. BMC genomics 7.1 (2006): 64.] that calculates the average mRNA copy number per cell, which allows researchers to directly compare gene expression intensities. By utilizing Percellome data, we examine the gene expression profiles among several organs in mice (liver, kidney, lung, brain and heart) after the oral administration of antiepileptic drug valproic acid sodium salt (VA) to infer the mechanism of its toxicity by identifying organ-specific reactions as well as pan-organ reactions. Although the hepatotoxicity of VA has been extensively investigated, its impacts on other organs are still remained to be elucidated.
Male mice (C57BL/6, 12 weeks old) were administered with VA (0, 50, 150, 500 mg/kg, vehicle: methyl cellulose 0.5%) and were sampled after 2, 4, 8, or 24 hr for microarray analysis (Affymetrix GeneChip Mouse Genome 430 2.0). We selected the genes whose expression intensities showed treatment time- and dose-dependencies in the liver, kidney, lung, brain or heart. The enriched features in these genes were investigated by using the pathway analysis features (“gadgets”) in the Garuda platform [Ghosh, S., et al. Nature Reviews Genetics 12.12 (2011): 821-832.]. Our results demonstrated that the activities of transcription factors associated with lipid metabolism (PPAR-alpha, SREBP) were affected in the liver by VA treatment. Furthermore, we detected pathways that were commonly enriched among these organs, and these pathways were associated with immune responses or cell cycle.