DomainGraph

Description

DomainGraph is a Java plugin for Cytoscape, a software platform for the analysis and visualization of molecular interaction networks.

The main functionality of the DomainGraph plugin is the visual analysis of the effects of alternative splicing on genes, protein isoforms, molecular interactions, pathways and miRNA binding sites. Statistical results of Exon Array and RNA-sequencing data computed with AltAnalyze can be imported into DomainGraph and affected genes, pathways and miRNA binding sites are automatically annotated. From these annotations, genes, gene products, and pathways can directly be loaded and visualized via DomainGraph and occurrences of alternative splicing are highlighted. Therefore, an in-depth analysis of Exon Array and RNA-sequencing data regarding alternative splicing events and their biological impact is easily possible without the need of prior knowledge.

Furthermore, the detailed analysis of interaction networks and pathways is possible. Given a gene interaction network, DomainGraph visualizes the genes together with all known encoded protein isoforms and their respective domain compositions. Given a protein interaction network, DomainGraph decomposes the proteins into their domains and visualizes the domain interactions underlying the protein interactions. These networks can be integrated with exon expression data produced by the Affymetrix Exon Array or RNA-sequencing. Genes, protein isoforms and domains are highlighted according to potentially occurring alternative splicing events or differential expression in different groups of samples.

Current Version

Release 3.01b, December 2018

Main features:

The plugin uses SSL for the server connection.
The plugin works with Cytoscape 2.6, and requires Java SE 8.

Release 3.01, December 2009

Main features:

Analysis of AltAnalyze Exon Array and RNA-sequencing data with regard to genes, protein isoforms, pathways, and miRNA binding sites affected by alternative splicing. No prior knowledge of potentially affected genes or pathways required.
Automatic annotation and visualization of genes, Reactome and WikiPathways, and miRNA binding sites with integrated Exon Array and RNA-sequencing data.
Decomposition of gene interaction networks into all known encoded protein isoforms and their domain compositions.
Decomposition of protein interaction networks into underlying domain interactions.
Integration of Affymetrix Human, Mouse, and Rat Exon Arrays (for differential expression analysis via AltAnalyze and expression studies for single experiments).
Graphical view of all protein isoforms encoded by a single gene with constituent domains, exon structures, Affymetrix probesets, and miRNA binding sites for convenient comparison of exon expression.
Annotation of microRNA binding sites for probesets.
Annotation of cross-hybridization types for probesets.
HTML export of AltAnalyze statistics with biological annotations (genes, pathways, miRNA binding sites, alternative exon annotations) with all gene and pathway graphics.

Former Versions

Release 1.0, April 2008

Release 2.01, December 2008

System Requirements

The plugin works with Cytoscape 2.6, and requires Java SE 6.

Download, Documentation and Tutorial

You can download the latest version of DomainGraph here.
The online documentation describing the features and databases used can be found here.
Click here for a detailed tutorial.

Reference

Emig, D, Salomonis, N, Baumbach, J, Lengauer, T, Conklin, BR, Albrecht, M. AltAnalyze and DomainGraph: analyzing and visualizing exon expression data. Nucleic Acids Research, 2010.
(Abstract)

Contributors

Dorothea Emig¹, Nathan Salomonis², Melissa S. Cline³, Jan Baumbach⁴, Thomas Lengauer¹, Bruce R. Conklin², Mario Albrecht¹

¹ Department of Computational Biology & Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
² The J. David Gladstone Institutes, San Francisco, CA, USA
³ Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
⁴ International Computer Science Institute, Berkeley, CA, USA

Other Plugins

We have also developed the following plugins:
- NetworkAnalyzer
- BiLayout
- NeighborHighlight

Contact

If you have any questions, comments, suggestions or criticism, feel free to contact us at: domaingraph [at] mpi-inf [dot] mpg [dot] de.