MetaboClust: Using interactive time-series cluster analysis to relate metabolomic data with perturbed pathways

Abstract

Motivation: Modern analytical techniques such as LC-MS, GC-MS and NMR are increasingly being used to study the underlying dynamics of biological systems by tracking changes in metabolite levels over time. Such techniques are capable of providing information on large numbers of metabolites simultaneously, a feature that is exploited in non-targeted studies. However, since the dynamics of specific metabolites are unlikely to be known a priori this presents an initial subjective challenge as to where the focus of the investigation should be. Whilst a number of feed-forward software tools are available for manipulation of metabolomic data, no tool centralizes on clustering and focus is typically directed by a workflow that is chosen in advance. Results: We present an interactive approach to time-course analyses and a complementary implementation in a software package, MetaboClust. This is presented through the analysis of two LC-MS time-course case studies on plants (Medicago truncatula and Alopecurus myosuroides). We demonstrate a dynamic, user-centric workflow to clustering with intrinsic visual feedback at all stages of analysis. The software is used to apply data correction, generate the time-profiles, perform exploratory statistical analysis and assign tentative metabolite identifications. Clustering is used to group metabolites in an unbiased manner, allowing pathway analysis to score metabolic pathways, based on their overlap with clusters showing interesting trends.