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Bioinformatics Advance Access published online on December 1, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm581
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© 2007 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.

KEGGanim: pathway animations for high-throughput data

Priit Adler a,*, Jüri Reimand b,*, Jürgen Jänes b, Raivo Kolde c, Hedi Peterson a,c and Jaak Vilo a,b,c,{dagger}

aEstonian Biocentre, Riia 23b, Tartu, Estonia bUniversity of Tartu, Institute of Computer Science, Liivi 2, Tartu, Estonia c QureTec Inc. Ülikooli 6a, Tartu, Estonia

{dagger}To whom correspondence should be addressed. Jaak Vilo, E-mail: vilo{at}ut.ee


  Abstract

Motivation: Gene expression analysis with microarrays has become one of the most widely used high-throughput methods for gathering genome-wide functional data. Emerging -omics fields such as proteomics and interactomics introduce new information sources. With the rise of systems biology, researchers need to concentrate on entire complex pathways that guide individual genes and related processes. Bioinformatics methods are needed to link the existing knowledge about pathways with the growing amounts of experimental data.

Results: We present KEGGanim, a novel web-based tool for visualising experimental data in biological pathways. KEGGanim produces animations and images of KEGG pathways using public or user uploaded high-throughput data. Pathway members are coloured according to experimental measurements, and animated over experimental conditions. KEGGanim visualisation highlights dynamic changes over conditions and allows the user to observe important modules and key genes that influence the pathway. The simple user interface of KEGGanim provides options for filtering genes and experimental conditions. KEGGanim may be used with public or private data for 14 organisms, with a large collection of publicmicroarray data readily available. Most common gene and protein identifiers and microarray probesets are accepted for visualisation input.

Availability: http://biit.cs.ut.ee/KEGGanim/.

Contact: vilo{at}ut.ee

Associate Editor: Dr. Olga Troyanskaya

*Authors contributed equally to this work and appear in alphabetical order.

Received on August 5, 2007; revised on October 22, 2007; accepted on November 19, 2007

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