Visualization of Graphs with Associated Timeseries Data
INFOVIS '05 Proceedings of the Proceedings of the 2005 IEEE Symposium on Information Visualization
Visualizing biological pathways: requirements analysis, systems evaluation and research agenda
Information Visualization - Special issue: Bioinformatics visualization
Dynamic exploration and editing of KEGG pathway diagrams
Bioinformatics
VisLink: Revealing Relationships Amongst Visualizations
IEEE Transactions on Visualization and Computer Graphics
Tools for visually exploring biological networks
Bioinformatics
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DNA microarrays are used to measure the expression levels of thousands of genes simultaneously. In a time series experiment, the gene expressions are measured as a function of time. We present an application for integrated visualization of genome expression and network dynamics in both regulatory networks and metabolic pathways. Integration of these two levels of cellular processes is necessary, since it provides the link between the measurements at the transcriptional level (gene expression levels approximated from microarray data) and the phenotype (the observable characteristics of an organism) at the functional and behavioral level. The integration requires visualization approaches besides traditional clustering and statistical analysis methods. Our application can (i) visualize the data from time series experiments in the context of a regulatory network and KEGG metabolic pathways; (ii) identify and visualize active regulatory subnetworks from the gene expression data; (iii) perform a statistical test to identify and subsequently visualize pathways that are affected by differentially expressed genes. We present a case study, which demonstrates that our approach and application both facilitates and speeds up data analysis tremendously in comparison to a more traditional approach that involves many manual, laborious, and error-prone steps.