Sangam: A Confluence of Knowledge Streams

Visualization and analysis of microarray and gene ontology data with treemaps

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dc.creator Baehrecke, Eric H
dc.creator Dang, Niem
dc.creator Babaria, Ketan
dc.creator Shneiderman, Ben
dc.date 2021-12-09T16:05:16Z
dc.date 2021-12-09T16:05:16Z
dc.date 2004-06-28
dc.date.accessioned 2022-05-20T08:38:34Z
dc.date.available 2022-05-20T08:38:34Z
dc.identifier https://doi.org/10.13016/xzka-isj2
dc.identifier Baehrecke, E.H., Dang, N., Babaria, K. et al. Visualization and analysis of microarray and gene ontology data with treemaps. BMC Bioinformatics 5, 84 (2004).
dc.identifier http://hdl.handle.net/1903/28230
dc.identifier.uri http://localhost:8080/xmlui/handle/CUHPOERS/117634
dc.description 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. 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. 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.
dc.description https://doi.org/10.1186/1471-2105-5-84
dc.format application/pdf
dc.language en_US
dc.publisher Springer Nature
dc.relation College of Computer, Mathematical & Physical Sciences
dc.relation Digital Repository at the University of Maryland
dc.relation Biology
dc.relation University of Maryland (College Park, MD)
dc.subject Gene Ontology
dc.subject Salivary Gland
dc.subject Control Panel
dc.subject Gene Node
dc.subject Quantitative Attribute
dc.title Visualization and analysis of microarray and gene ontology data with treemaps
dc.type Article


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