Journal Article

Caleydo: connecting pathways and gene expression

Marc Streit, Alexander Lex, Michael Kalkusch, Kurt Zatloukal and Dieter Schmalstieg

in Bioinformatics

Volume 25, issue 20, pages 2760-2761
Published in print October 2009 | ISSN: 1367-4803
Published online July 2009 | e-ISSN: 1460-2059 | DOI:

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Summary: Understanding the relationships between pathways and the altered expression of their components in disease conditions can be addressed in a visual data analysis process. Caleydo uses novel visualization techniques to support life science experts in their analysis of gene expression data in the context of pathways and functions of individual genes. Pathways and gene expression visualizations are placed in a 3D scene where selected entities (i.e. genes) are visually connected. This allows Caleydo to seamlessly integrate interactive gene expression visualization with cross-database pathway exploration.

Availability: The Caleydo visualization framework is freely available on for non-commercial use. It runs on Windows and Linux and requires a 3D capable graphics card.


Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  996 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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