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

Michel A. Westenberg*, Sacha A.F.T. van Hijum, Andrzej T. Lulko, Oscar P. Kuipers, Jos B.T.M. Roerdink

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference contributionAcademicpeer-review

2 Citations (Scopus)
357 Downloads (Pure)

Abstract

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.

Original languageEnglish
Title of host publicationVISUALIZATION IN MEDICINE AND LIFE SCIENCES
EditorsL Linsen, H Hagen, B Hamann
Place of PublicationBERLIN
PublisherSpringer
Pages293-+
Number of pages20
ISBN (Print)978-3-540-72629-6
Publication statusPublished - 2008
EventWorkshop on Visualization in Medicine and Life Sciences - , Germany
Duration: 1-Jul-2006 → …

Publication series

NameMATHEMATICS AND VISUALIZATION
PublisherSPRINGER-VERLAG BERLIN
ISSN (Print)1612-3786

Other

OtherWorkshop on Visualization in Medicine and Life Sciences
Country/TerritoryGermany
Period01/07/2006 → …

Keywords

  • BACILLUS-SUBTILIS
  • CATABOLITE REPRESSION
  • ANALYSIS TOOL
  • CCPA
  • BIOLOGY
  • VISANT
  • LAYOUT

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