{[ promptMessage ]}

Bookmark it

{[ promptMessage ]}

Extending MapMan_application to legume genome arrays

Extending MapMan_application to legume genome arrays -...

Info icon This preview shows pages 1–2. Sign up to view the full content.

View Full Document Right Arrow Icon
Vol. 22 no. 23 2006, pages 2958–2959 doi:10.1093/bioinformatics/btl517 BIOINFORMATICS APPLICATIONS NOTE Gene expression Extending MapMan: application to legume genome arrays Nicolas Goffard and Georg Weiller à 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: [email protected] 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.
Image of page 1

Info icon This preview has intentionally blurred sections. Sign up to view the full version.

View Full Document Right Arrow Icon
Image of page 2
This is the end of the preview. Sign up to access the rest of the document.

{[ snackBarMessage ]}

What students are saying

  • Left Quote Icon

    As a current student on this bumpy collegiate pathway, I stumbled upon Course Hero, where I can find study resources for nearly all my courses, get online help from tutors 24/7, and even share my old projects, papers, and lecture notes with other students.

    Student Picture

    Kiran Temple University Fox School of Business ‘17, Course Hero Intern

  • Left Quote Icon

    I cannot even describe how much Course Hero helped me this summer. It’s truly become something I can always rely on and help me. In the end, I was not only able to survive summer classes, but I was able to thrive thanks to Course Hero.

    Student Picture

    Dana University of Pennsylvania ‘17, Course Hero Intern

  • Left Quote Icon

    The ability to access any university’s resources through Course Hero proved invaluable in my case. I was behind on Tulane coursework and actually used UCLA’s materials to help me move forward and get everything together on time.

    Student Picture

    Jill Tulane University ‘16, Course Hero Intern