Temporal pathway activity analysis of transcriptional profiling of in utero exposure to d-n-butyl phthalate
M. Ovacik1, M.G. Ierapetritou1, P.G. Georgopoulos2, W. Welsh2, S. Euling3, B. Sen3, K. Gaido4 and I.P. Androulakis1
1Rutgers University, 2UDMNJ-RWJMS, 3USEP, 4CIIT
In this study, we explore a novel extension of the pathway activity methodology1 and use it on temporal transcriptional profiling and demonstrate its applicability in the context of evaluating possible toxicity mechanisms of Di-n-butyl phthalate (DBP). Studies in rats and mice have shown that oral exposure to DBP results in developmental toxicity in male reproductive organs. Furthermore, transcriptional studies have demonstrated that DBP represses the expression of genes involved in cholesterol transport, steroid biosynthesis and testosterone synthesis A previous microarray study2 using DBP exposure focused on individual genes which showed a significant change in expression..However, an alternative approach, which is pursued in this study, focusses on the genes that are known to be members of metabolic and signaling pathways. The pathway activity level (PAL) analysis entails a singular value decomposition (SVD) of the expression data of the genes constituting a given pathway. The activity level of a pathway is therefore the weighted sum of gene expression of individual genes in the given pathway and represents the change of all gene expressions in a given pathway regardless of specifying up or down regulation. The microarray study has both control and treated profiles over time which enables us to include the temporal changes of control profile into the analysis. Our methodology led to biologically relevant results such that C21-Steroid hormone metabolism, biosynthesis of steroids and PPAR signaling pathway were identified as active pathways due to DBP exposure. In addition, we were able to monitor the temporal evaluation of pathway activities and cluster the active pathways based on their temporal evaluation.
1Tomfohr J. et al. BMC Bioinf., 2005. 6:225
2Thompson CJ. et al. Biol Reprod, 2005. 73:908-17