MapMan

MapMan maps gene expression and metabolite datasets from Arabidopsis Affymetrix 22K arrays onto metabolic pathway and biological process diagrams to visualize and analyze molecular responses such as sugar starvation.

Key Features:

• Hierarchical Categorization: SCAVENGER modules assign measured parameters into hierarchical BINs and subBINs, resolving central and secondary metabolism down to individual enzymes.
• Gene Grouping (TRANSCRIPTSCAVENGER): TRANSCRIPTSCAVENGER groups genes from the Arabidopsis Affymetrix 22K array into over 200 hierarchical categories.
• Metabolite Organization (METABOLITESCAVENGER): METABOLITESCAVENGER groups hundreds of metabolites into pathways or structurally related compound sets.
• Customizable Visualization (IMAGEANNOTATOR): IMAGEANNOTATOR organizes and displays experimental datasets onto user-defined pathway and process diagrams.
• Modular Structure: A modular architecture allows editing and addition of categories and development of SCAVENGER modules for different data types.

Scientific Applications:

• Sugar-depletion transcriptome analysis in Arabidopsis rosettes: Applied to two sets of 22K Affymetrix arrays (a six-hour night extension and a comparison of wild-type Columbia-0 (Col-0) versus the starchless pgm mutant at the end of the night), revealing repression of photosynthesis, nutrient acquisition, and biosynthetic genes and induction of amino acid, nucleotide, lipid, and cell wall catabolic genes.
• Regulatory and signaling network analysis: Identified changes in trehalose metabolism suggesting trehalose-6-phosphate (Tre6P) as a starvation signal and widespread alterations in receptor kinases, transcription factors, signaling pathways, post-translational modifications, and cytokinin, abscisic acid (ABA), and ethylene synthesis and sensing indicative of regulatory network rewiring.

Methodology:

Measured parameters are assigned to BINs/subBINs by SCAVENGER modules; genes are grouped by TRANSCRIPTSCAVENGER; metabolites are grouped by METABOLITESCAVENGER; and datasets are mapped onto pathway/process diagrams via IMAGEANNOTATOR.