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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

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Journal of Biological Research-Thessaloniki

ISSN: 2241-5793

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