exploRase: Exploratory data analysis of systems biology data

Michael Lawrence, Eun Kyung Lee, Dianne Cook, Heike Hofmann, Eve Wurtele

Research output: Chapter in Book/Report/Conference proceedingConference PaperOtherpeer-review

6 Citations (Scopus)

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 metaholomic 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 implictly linking views across datasets via network relationships and integrating exploRase with more diverse view types.

Original languageEnglish
Title of host publicationProceedings - Fourth International Conference on Coordinated and Multiple Views in Exploratory Visualization, CMV 2006
Pages14-20
Number of pages7
Volume2006
DOIs
Publication statusPublished - 1 Dec 2006
Event4th International Conference on Coordinated and Multiple Views in Exploratory Visualization, CMV 2006 - London, United Kingdom
Duration: 4 Jul 20064 Jul 2006

Conference

Conference4th International Conference on Coordinated and Multiple Views in Exploratory Visualization, CMV 2006
CountryUnited Kingdom
CityLondon
Period4/07/064/07/06

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