Integrating expression data with domain interaction networks

Abstract

Recent studies have revealed that alternative splicing plays an important role in the observed protein and interaction diversity. Special microarrays allow for measuring gene expression at the exon level and thus for studying alternative transcripts and their corresponding protein domain architecture. We have developed the Cytoscape plugin DomainGraph that enables the visualization and detailed study of domain-domain interactions forming protein interaction networks. In addition, the integration of exon expression data supports the analysis of alternative splicing events and the characterization of their effects on the protein and domain interaction network. Different expression patterns between human tissues or cells can be identified by comparing the generated domain graphs.

Availability: The plugin DomainGraph and the online documentation are available at http://domaingraph.bioinf.mpi-inf.mpg.de.

Fig. 1.

The extended view of a domain graph consisting of protein (rectangle) and domain (diamond) nodes. The nodes are colored according to the integrated Affymetrix exon data. Domains affected by alternative splicing are colored pink, and domains forming interactions with spliced domains are colored orange. Gray nodes represent proteins belonging to unexpressed genes. Hovering the mouse over a node displays a tooltip and highlights the direct node interaction partners in red color. In the Attribute Browser at the bottom, the domain architecture (top line, only with CDS) and exon structure (middle line, including both CDS and 3′ - and 5′ -UTRs) of the protein selected by the user is shown together with the probesets (bottom line), which are colored according to the respective expression level.