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Interactive visualization of gene regulatory networks with associated gene expression time series data. (English) Zbl 1255.68272
Linsen, Lars (ed.) et al., Visualization in medicine and life sciences. Selected papers based on the presentations at the workshop, Rügen, Germany, July 2006. Berlin: Springer (ISBN 978-3-540-72629-6/hbk). Mathematics and Visualization, 293-311 (2008).
Summary: We present GENeVis, an application to visualize gene expression time series data in a gene regulatory network context. This is a network of regulator proteins that regulate the expression of their respective target genes. The networks are represented as graphs, in which the nodes represent genes, and the edges represent interactions between a gene and its targets. GENeVis adds features that are currently lacking in existing tools, such as mapping of expression value and corresponding p-value (or other statistic) to a single visual attribute, multiple time point visualization, and visual comparison of multiple time series in one view. Various interaction mechanisms, such as panning, zooming, regulator and target highlighting, data selection, and tooltips support data analysis and exploration. Subnetworks can be studied in detail in a separate view that shows the network context, expression data plots, and tables containing the raw expression data. We present a case study, in which gene expression time series data acquired in-house are analyzed by a biological expert using GENeVis. The case study shows that the application fills the gap between present biological interpretation of time series experiments, performed on a gene-by-gene basis, and analysis of global classes of genes whose expression is regulated by regulator proteins.
For the entire collection see [Zbl 1124.92001].
Reviewer: Reviewer (Berlin)
68U10 Computing methodologies for image processing
62M10 Time series, auto-correlation, regression, etc. in statistics (GARCH)
92C50 Medical applications (general)