Visualization and analysis of microarray and gene ontology data with treemaps

Eric H Baehrecke¹ , Niem Dang² , Ketan Babaria² and Ben Shneiderman²

¹Center for Biosystems Research, University of Maryland Biotechnology Institute, College Park, Maryland 20742, USA

²Department of Computer Science and Human-Computer Interaction Laboratory, University of Maryland, College Park, Maryland 20742, USA

author email corresponding author email

BMC Bioinformatics 2004, 5:84doi:10.1186/1471-2105-5-84


Published:	28 June 2004

Abstract

Background

The increasing complexity of genomic data presents several challenges for biologists. Limited computer monitor views of data complexity and the dynamic nature of data in the midst of discovery increase the challenge of integrating experimental results with information resources. The use of Gene Ontology enables researchers to summarize results of quantitative analyses in this framework, but the limitations of typical browser presentation restrict data access.

Results

Here we describe extensions to the treemap design to visualize and query genome data. Treemaps are a space-filling visualization technique for hierarchical structures that show attributes of leaf nodes by size and color-coding. Treemaps enable users to rapidly compare sizes of nodes and sub-trees, and we use Gene Ontology categories, levels of RNA, and other quantitative attributes of DNA microarray experiments as examples. Our implementation of treemaps, Treemap 4.0, allows user-defined filtering to focus on the data of greatest interest, and these queried files can be exported for secondary analyses. Links to model system web pages from Treemap 4.0 enable users access to details about specific genes without leaving the query platform.

Conclusions

Treemaps allow users to view and query the data from an experiment on a single computer monitor screen. Treemap 4.0 can be used to visualize various genome data, and is particularly useful for revealing patterns and details within complex data sets.