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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 http://vis.usal.es/bicoverlapper/
BiGGEsTS Heat map-based bicluster visualisation http://tinyurl.com/BiGGEsTS
Brain Explorer Visualisation of 3D transcription data in the central nervous system http://tinyurl.com/brainExplorer
Data Matrix Viewer Simple profile plot visualisation; supports Gaggle http://gaggle.systemsbiology.net/
EXPANDER Heat maps, scatter plots and profile plots of cluster averages http://acgt.cs.tau.ac.il/expander
GENESIS Analysis suite; offers several interactive visualisations http://genome.tugraz.at/
geWorkbench Modular suite; heat maps, dendrograms, profile and scatter plots http://tinyurl.com/geWorkbench
Hierarchical Clustering Explorer Linked heat map, profile and scatter plots; systematic exploration http://tinyurl.com/HCExplorer
Java TreeView Linked heat maps, karyoscopes, sequence alignments, scatter plots http://jtreeview.sourceforge.net/
Mayday Modular suite; many linked visualisations; enhanced heat map113 http://tinyurl.com/maydaywp
MultiExperiment Viewer Analysis suite; heat maps, dendrograms, profile and scatter plots http://www.tm4.org/
PointCloudXplore Visualisation of 3D transcription data in Drosophila embryos http://tinyurl.com/PointCloudXplore
TimeSearcher Exploration and analysis of time series; advanced profile plots http://tinyurl.com/timesearcher
R/BioConductor Geneplotter Karyoscope-style plots and other visualisations http://www.bioconductor.org/
GenePattern Modular analysis platform; several visualisation modules available http://tinyurl.com/GenePatt
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 http://www.cytoscape.org/index.html