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Bioinformatics Advance Access originally published online on July 20, 2009
Bioinformatics 2009 25(20):2760-2761; doi:10.1093/bioinformatics/btp432
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© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Caleydo: connecting pathways and gene expression

Marc Streit 1,*, Alexander Lex 1, Michael Kalkusch 1, Kurt Zatloukal 2 and Dieter Schmalstieg 1

1 Institute for Computer Graphics and Vision, Graz University of Technology, Inffeldgasse 16 and 2 Institute of Pathology, Medical University Graz, Auenbruggerplatz 25, 8010 Graz, Austria

* To whom correspondence should be addressed.


  Abstract

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 www.caleydo.org for non-commercial use. It runs on Windows and Linux and requires a 3D capable graphics card.

Contact: caleydo{at}icg.tugraz.at; streit{at}icg.tugraz.at

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Olga Troyanskaya

Received on March 16, 2009; revised on June 29, 2009; accepted on July 13, 2009

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