FORG3D: force-directed 3D graph editor for visualization of integrated genome scale data - PubMed (original) (raw)

FORG3D: force-directed 3D graph editor for visualization of integrated genome scale data

Jussi Paananen et al. BMC Syst Biol. 2009.

Abstract

Background: Genomics research produces vast amounts of experimental data that needs to be integrated in order to understand, model, and interpret the underlying biological phenomena. Interpreting these large and complex data sets is challenging and different visualization methods are needed to help produce knowledge from the data.

Results: To help researchers to visualize and interpret integrated genomics data, we present a novel visualization method and bioinformatics software tool called FORG3D that is based on real-time three-dimensional force-directed graphs. FORG3D can be used to visualize integrated networks of genome scale data such as interactions between genes or gene products, signaling transduction, metabolic pathways, functional interactions and evolutionary relationships. Furthermore, we demonstrate its utility by exploring gene network relationships using integrated data sets from a Caenorhabditis elegans Parkinson's disease model.

Conclusion: We have created an open source software tool called FORG3D that can be used for visualizing and exploring integrated genome scale data.

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Figures

Figure 1

Figure 1

Graph editor. Various aspects of the data can be visualized by changing the visual appearance and physical properties of nodes and edges. Graph editor can be used to control these properties, structure of the network and different simulation options.

Figure 2

Figure 2

Integrated C. elegans data network. (A) In the visualized network, nodes represent genes and edges represent interactions between the genes. Measured fold change in gene expression was used to set the color of the nodes, green indicating up regulation, red indicating down regulation and yellow indicating no change between samples. Size of the nodes represents the number of Gene Ontology classes assigned to a gene. Query genes used to create the genetic interaction data are visualized as blue cubes. Width and spring constant of the edges represent interaction strength, and the color represents the screening method that was used to evaluate the interaction between the genes, blue for Byrne et al. and violet for Lehner et al. Because of the large number of the edges, only the edges with strongest interactions were set to visible (interaction strength > 5). (B) The hub node representing the daf-2 gene was selected and dragged to the side. Other nodes followed according to the strength of the edges as determined by the spring constant. Notice discrete groups of connected nodes representing genes directly connected to daf-2, and genes indirectly connected to daf-2. In the actual real-time simulation the movement speed and direction of the nodes are clear indications of the strength and structure of the interaction network.

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