Visualization and analysis of microarray and gene ontology data with treemaps

BackgroundThe 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.ResultsHere 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.ConclusionsTreemaps 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.

[1]  Ben Shneiderman,et al.  Ordered and quantum treemaps: Making effective use of 2D space to display hierarchies , 2002, TOGS.

[2]  Ben Shneiderman,et al.  Tree visualization with tree-maps: 2-d space-filling approach , 1992, TOGS.

[3]  Joaquín Dopazo,et al.  FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes , 2004, Bioinform..

[4]  Ronald W. Davis,et al.  Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray , 1995, Science.

[5]  D. Botstein,et al.  Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[6]  C. Thummel,et al.  A steroid-triggered transcriptional hierarchy controls salivary gland cell death during Drosophila metamorphosis. , 2000, Molecular cell.

[7]  S. Schreiber,et al.  Printing proteins as microarrays for high-throughput function determination. , 2000, Science.

[8]  May D. Wang,et al.  GoMiner: a resource for biological interpretation of genomic and proteomic data , 2003, Genome Biology.

[9]  Yigong Shi,et al.  Mechanisms of caspase activation and inhibition during apoptosis. , 2002, Molecular cell.

[10]  Steven C. Lawlor,et al.  MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data , 2003, Genome Biology.

[11]  J. Yates,et al.  Direct analysis of protein complexes using mass spectrometry , 1999, Nature Biotechnology.

[12]  C. Thummel,et al.  The Drosophila E93 gene from the 93F early puff displays stage- and tissue-specific regulation by 20-hydroxyecdysone. , 1995, Developmental biology.

[13]  C. Thummel,et al.  Steroid regulated programmed cell death during Drosophila metamorphosis. , 1997, Development.

[14]  Tanya M. Teslovich,et al.  Genome-Wide Analyses of Steroid- and Radiation-Triggered Programmed Cell Death in Drosophila , 2003, Current Biology.

[15]  Simon M. Lin,et al.  Applications of Tree-Maps to hierarchical biological data , 2002, Bioinform..

[16]  M. Gerstein,et al.  Global Analysis of Protein Activities Using Proteome Chips , 2001, Science.

[17]  D. Lockhart,et al.  Expression monitoring by hybridization to high-density oligonucleotide arrays , 1996, Nature Biotechnology.

[18]  C. Thummel,et al.  E93 directs steroid-triggered programmed cell death in Drosophila. , 2000, Molecular cell.

[19]  J. Blake,et al.  Creating the Gene Ontology Resource : Design and Implementation The Gene Ontology Consortium 2 , 2001 .