Challenge: The client had performed complex time-course bulk RNA-seq experiments performed on cells exposed to a number of different chemicals at a range of concentrations over the course of 12 days. Standard pairwise differential gene expression had been performed but could not capture all the information in the complex experimental design used in the experiment. The client requested help to evaluate alternative methods of analysing complex time course experiments.
Solution: A survey of state-of-the-art tools was performed and two selected for application to the dataset. Genes with significantly different expression profiles were identified using both approaches, pathway enrichment performed and the usability and performance of the tools assessed. Visualisation of pathway enrichment across doses allowed the effect of dose response to be captured.
Impact: The customer was provided with a comprehensive report detailing the results obtained as well as an assessment of the tools, allowing the customer to make an informed decision about which results to take forward for publication of their study.