Expression Analysis Tools

eFP browser | MapMan | Metabolic Pathways | PLEXdb

The electronic Fluorescent Pictograph Browser (eFP browser) was developed by Nicholas Provart and colleagues at the Bio-Array Resource for Plant Biology at the University of Toronto. The eFP browser projects gene expression data onto a series of pictures (pictographs) representing the original plant tissues from which the expression data was derived. Each pictograph is colored according to the level of expression for the gene on of interest. The eFP browser can analyze a single gene across a variety of plant tissues or single tissue undergoing a series of stress treatments (heat, drought, insect and pathogen infection, etc.).

The current Maize eFP browser contains expression as reported by Sekhon et al 2011 mapped to B73 RefGen_v2. For an example use, "Expression: See the eFP Browser" link on GRMZM2G165390 (bz1) and other gene model pages

MapMan was developed at the Max Planck Institute for Molecular Plant Physiology in Potsdam, Germany. The MapMan software suite allows the visualization of a variety of functional genomics datasets (gene expression, protein, enzyme, and metabolite levels) in the context of a large number of well characterized biochemical processes and metabolic pathways. A key strength of MapMan is its focus on plant specific processes and it capabilities for cross-species (e.g. maize vs. rice, etc.) comparisons.

The following pages allow users to download expression files from the "Genome-wide atlas of transcription during maize development" study by Sekhon et al 2011. The files can be imported into the MapMan software and visualized in different pathways that are available in MapMan

Metabolic Pathways

Metabolic pathways are represented by MaizeCyc ver 2.0, which is a comprehensive database of metabolic pathways that contains 39,656 proteins and 390 pathways. MaizeCyc v2.0 is created in collaboration with Gramene and MaizeGDB. MaizeCyc has an “Omics Viewer” that allows users to display their expression data painted on pathways, where each protein colored according to its expression level.

Tutorials
+ Gramene
+ BioCyc

PLEXdb (Plant Expression Database) is a gene expression resource for plants and plant pathogens which combines a large and increasing collection of curated gene expression data sets for many array platformsdesigns by multiple vendors, including Affymetrix, NimbleGen, with a set of visualization and analysis tools, including the Experiment Browser and the Gene List Suite. The maize specific resources can be accessed at the MaizePLEX page.

Publication

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Last updated 6:00 pm, Dec 31, 1969.