exploRase: Exploratory Data Analysis of Systems Biology Data

Abstract

exploRase is a software tool for the exploratory analysis of systems biology data. Exploration of complex biochemical systems requires the integration of experimental data, such as transcriptomic, proteomic, and metabolomic data, with biochemical networks. The networks specify the relationships between the entities (transcripts, proteins, metabolites) described by the "omics" data and therefore serve as a unifying framework for the analysis. exploRase delegates to the interactive graphics platform GGobi for the display of the experimental data in scatterplots, parallel coordinate plots, barcharts, and more. The plots are interlinked so that brushing an entity in one plot will result in its being brushed in the others. The GGobi plots are linked to a network display, so that corresponding node glyphs in the network are also brushed. exploRase provides a graphical user interface (GUI) with tables containing entity metadata fields, such as biological function. The tables have a color column that is synchronized with the brushing of the GGobi plots and the network view. We demonstrate the usefulness of exploRase by analyzing a transcriptomic dataset that compares a biotin-deficient Arabidopsis mutant with the wildtype. The next steps in development include implicitly linking views across datasets via network relationships and integrating exploRase with more diverse view types