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Bioinformatics Advance Access originally published online on August 18, 2008
Bioinformatics 2008 24(21):2546-2548; doi:10.1093/bioinformatics/btn437
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Integrating expression data with domain interaction networks

Dorothea Emig 1, Melissa S. Cline 2, Thomas Lengauer 1 and Mario Albrecht 1,*

1Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Campus E1.4, 66123 Saarbrücken, Germany and 2Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA 95064, USA

*To whom correspondence should be addressed.


  Abstract

Summary: 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.

Contact: mario.albrecht{at}mpi-inf.mpg.de

Associate Editor: Trey Ideker

Received on April 24, 2008; revised on July 22, 2008; accepted on August 15, 2008

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