DomainGraphDemo: Visual Analysis of the Effects of Alternative Splicing on Protein and Domain Interaction Networks
Dorothea Emig1, Melissa S. Cline2, Thomas Lengauer1, and Mario Albrecht1
1 Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Campus E1.4, 66123 Saarbrücken, Germany 2 Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
DomainGraph is a Cytoscape plugin that supports an integrative analysis and visualization of protein and domain interaction networks together with exon expression data. DomainGraph comprises two main functionalities: (1) the visual decomposition of a user-imported protein interaction network into the underlying domain-domain interactions and (2) the integration of Affymetrix Human Exon 1.0 ST Array expression data for highlighting protein domains and their interactions affected by alternative splicing events.
DomainGraph supports the decomposition into domain interactions for twelve species, and provides several structure-based and predicted domain interaction datasets. When integrating exon expression data into the network, domains are colored differently if they are partly or completely missing due to alternative splicing events. Additional information provided for the user includes the graphical representation of the protein domain architectures, the underlying exon structures, probeset annotations, and GO and OMIM annotations.
Our approach allows the user to easily detect occurrences of alternative splicing and to investigate their effects on the protein and domain network. Additional analysis methods for the graphical comparison of domain graphs help to unveil similarities and dissimilarities in expression patterns of different tissues or cells.
The DomainGraph plugin and a comprehensive online documentation with a tutorial are available at http://domaingraph.bioinf.mpi-inf.mpg.de
Data keywords: protein-protein interaction, domain-domain interaction, alternative splicing, exon expression, Affymetrix Human Exon 1.0 ST Array
Cytoscape keywords: Network and Attribute I/O, Network Inference, Visual Style