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Table 4 Common visualisation tools in the area of “Interaction Network Visualisation”

From: Data integration in biological research: an overview

Name of resource What it does URL
BicOverlapper Visualisation of biclusters combined with profile plots and heat maps
BiGGEsTS Heat map-based bicluster visualisation
Brain Explorer Visualisation of 3D transcription data in the central nervous system
Data Matrix Viewer Simple profile plot visualisation; supports Gaggle
EXPANDER Heat maps, scatter plots and profile plots of cluster averages
GENESIS Analysis suite; offers several interactive visualisations
geWorkbench Modular suite; heat maps, dendrograms, profile and scatter plots
Hierarchical Clustering Explorer Linked heat map, profile and scatter plots; systematic exploration
Java TreeView Linked heat maps, karyoscopes, sequence alignments, scatter plots
Mayday Modular suite; many linked visualisations; enhanced heat map113
MultiExperiment Viewer Analysis suite; heat maps, dendrograms, profile and scatter plots
PointCloudXplore Visualisation of 3D transcription data in Drosophila embryos
TimeSearcher Exploration and analysis of time series; advanced profile plots
R/BioConductor Geneplotter Karyoscope-style plots and other visualisations
GenePattern Modular analysis platform; several visualisation modules available
Cytoscape Open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data