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Bioinformatics. 2006 Dec 1;22(23):2958-9. Epub 2006 Oct 17.

Extending MapMan: application to legume genome arrays.

Author information

  • 1ARC 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.

Abstract

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/

PMID:
17046975
[PubMed - indexed for MEDLINE]
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