Quantitative knowledge-based analysis in compound safety assessment

Areas covered: Current performance issues with statistical analysis of OMICs data or gene/protein/compound lists are discussed, illustrating potential advantages of knowledge-based approaches in prediction of human toxicity. The authors show several examples of quantitative functional analysis, including cross-tissue toxicity predictions and integrated analysis of different types of OMICs data. They also describe novel approaches linking compound targets and associated pathways to side effects. The reader will gain an update on the recent developments in knowledge-based analysis in toxicogenomics and computational methods correlating protein targets with adverse reactions. Expert opinion: Quantitative pathway analysis is a useful approach for deriving multi-variant predictive biomarkers for drug safety. However, more comprehensive studies are needed for direct comparison of performance between pathway- and gene-centric methods.