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Unformatted text preview: Vol. 22 no. 23 2006, pages 29582959 doi:10.1093/bioinformatics/btl517 BIOINFORMATICS APPLICATIONS NOTE Gene expression 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 Received on June 22, 2006; revised and accepted on October 5, 2006 Advance Access publication October 17, 2006 Associate Editor: David Rocke 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 organ- ism 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: firstname.lastname@example.org 1 INTRODUCTION Microarrays enable us to study the expression of thousands of genes simultaneously, providing a comprehensive overview of the gene activities in a given tissue. Bioinformatics tools, such as MapMan, can display this data in a functional context (Thimm et al ., 2004; Usadel et al ., 2005). MapMan requires three types of information: (1) a hierarchical classification of genes (i.e. BINs), (2) images representing a functional context of these genes (e.g. metabolic pathways) and (3) experimental expression data. The transcriptional activities of the binned genes are then displayed on the images using various statistical representations. Although initially developed for Arabidopsis thaliana arrays, MapMan can be extended to other systems by assigning new sequences to their orthologs in the current A.thaliana BINs (Urbanczyk-Wochniak et al ., 2006). However, this approach is limited as sequence similarity may be marginal with organisms of interest....
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This note was uploaded on 08/01/2009 for the course HORT hor-11-12 taught by Professor Park during the Spring '09 term at A.T. Still University.
- Spring '09