M.: Interactive visualization of gene regulatory networks with associated gene expression time series data

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 rep-resent interactions between a gene and its targets. GENeVis adds features that are currently lacking in existing tools, such as mapping of expression value and corre-sponding 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 in-teraction 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 bio-logical 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.