mapman: a user‐driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes

Abstract

SummaryMAPMAN is a user-driven tool that displays large data sets onto diagrams of metabolic pathways or other processes. SCAVENGER modules assign the measured parameters to hierarchical categories (formed`BINs', subBINs'). A ®rst build of TRANSCRIPTSCAVENGER groups genes on the Arabidopsis Affymetrix 22K array into >200 hierarchical categories, providing a breakdown of central metabolism (for several pathways, down to the single enzyme level), and an overview of secondary metabolism and cellular processes. METABOLITE-SCAVENGER groups hundreds of metabolites into pathways or groups of structurally related compounds. An IMAGEANNOTATOR module uses these groupings to organise and display experimental data sets onto diagrams of the users' choice. A modular structure allows users to edit existing categories, add new categories and develop SCAVENGER modules for other sorts of data. MAPMAN is used to analyse two sets of 22K Affymetrix arrays that investigate the response of Arabidopsis rosettes to low sugar: one investigates the response to a 6-h extension of the night, and the other compares wild-type Columbia-0 (Col-0) and the starchless pgm mutant (plastid phosphoglucomutase) at the end of the night. There were qualitatively similar responses in both treatments. Many genes involved in photosynthesis, nutrient acquisition, amino acid, nucleotide, lipid and cell wall synthesis, cell wall modi®cation, and RNA and protein synthesis were repressed. Many genes assigned to amino acid, nucleotide, lipid and cell wall breakdown were induced. Changed expression of genes for trehalose metabolism point to a role for trehalose-6-phosphate (Tre6P) as a starvation signal. Widespread changes in the expression of genes encoding receptor kinases, transcription factors, components of signalling pathways, proteins involved in post-translational modi®cation and turnover, and proteins involved in the synthesis and sensing of cytokinins, abscisic acid (ABA) and ethylene revealing large-scale rewiring of the regulatory network is an early response to sugar depletion.

A workflow to increase the detection rate of proteins from unsequenced organisms in high‐throughput proteomics experiments

“…Abbreviations are: CPSF, cleavage and polyadenylation specificity factor; NPACa, nascent polypeptide-associated complex alpha; eIF, eukaryotic initiation factor; EF, elongation factor; AAAATPase, ATPases associated with diverse cellular activities; ARFrelated proteins, ADP ribosylation factor-related proteins. The MapMan tool [30] was used to generate parts of this figure. tiple glycines, because they are likely derived from keratin. Furthermore, the user may consider accepting only those alignments that are based on two or more different peptides, in order to minimize the protein inference problem.…”

Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

“…Functional enrichment was analyzed using Mapman 82 . MapMan bins of the TM-1 genome were assigned by the Mercator pipeline for automated sequence annotation (http://mapman.…”

A comparative transcriptomic approach to understanding the formation of cork

“…The expression levels for all contigs are provided in Table S1. Contigs were also annotated with the Mercator tool using default parameters (http://mapman.gabipd.org/web/guest/mercator) to obtain the MapMan functional categories ('bins') (Thimm et al 2004).…”