Extending MapMan: application to legume genome arrays.
BACKGROUND
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.


BACKGROUND
All mapping files, pathway pictures and the analysis method are available at http://bioinfoserver.rsbs.anu.edu.au/
Goffard
Nicolas
N
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.
Weiller
Georg
G
D000465:Algorithms; D017360:Arabidopsis / Q000502:physiology*; D029681:Arabidopsis Proteins / Q000502:physiology*; D002874:Chromosome Mapping / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
D029681:Arabidopsis Proteins