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Bioinformatics Advance Access originally published online on October 17, 2006
Bioinformatics 2006 22(23):2958-2959; doi:10.1093/bioinformatics/btl517
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© 2006 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.

Extending MapMan: application to legume genome arrays

Nicolas Goffard and Georg Weiller *

ARC Centre of Excellence for Integrative Legume Research and Bioinformatics Laboratory, Genomic Interactions Group, Research School of Biological Sciences, Australian National University GPO Box 475, Canberra, ACT 2601, Australia

*To whom correspondence should be addressed.

Motivation: Based on a gene classification into hierarchical categories (‘BINs’), MapMan was originally developed to display Arabidopsis thaliana gene expression in a functional context. We have created a bioinformatics system to extend MapMan to any organism by using a new BIN structure based on the KEGG database. Gene sequences are assigned to this ontology by homology relationships in four reference databases: KEGG, COG, Swiss-Prot and Gene Ontology. We applied this system to tailor MapMan to the GeneChips of two model legumes, Glycine max and Medicago truncatula. We also developed a module to identify the most relevant pathways involved.

Availability: All mapping files, pathway pictures and the analysis method are available at http://bioinfoserver.rsbs.anu.edu.au/

Contact: georg.weiller{at}anu.edu.au

Received on June 22, 2006; revised on October 5, 2006; accepted on October 5, 2006

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