Plant MetGenMAP

Plant MetGenMAP is a visualization and analysis package that allows to identify changed pathways and enriched GO terms from gene expression and/or metabolite profile data and to visualize the profile data in a biochemical pathway context. You need to login to upload and analysis your data. New users please register to obtain an account. More information of the system can be obtained from the help page.

Currently the system supports the following organisms and platforms (identifiers). A list of example input files for each platform are provided in the help page.

Organism Pathways Platform

Arabidopsis AraCyc Arabidopsis ATH1 array
TAIR AGI Locus Number

Rice RiceCyc Affymetix genome array
Locus Number

Maize MaizeCyc Genome locus

Tomato LycoCyc Genome locus

TOM1 cDNA array

TOM2 oligo array Due to the multiple printing formats of TOM2 arrays, the system has to use Plate IDs as the unified ID system. If you are using CGEP printed probe IDs, you can convert them to plate IDs by clicking the link.

Affymetrix genome array

poplar PoplarCyc Genome locus

soybean Genome locus

sorghum Genome locus

Brachypodium Genome locus

grape Genome locus

papaya Genome locus

apple Genome locus

banana Genome locus

watermelon Genome locus

Chinese cabbage Genome locus

melon Genome locus

strawberry Genome locus

News
*Gene annotation updated* -- Gene annotations were updated with the AHRD pipeline. [Sept. 2013]
*Melon and strawberry genomes added* -- Pathways predicted from melon and strawberry genomes were added to the system [April. 2013]
*Tomato and Chinese cabbage genomes added* -- Pathways predicted from tomato and Chinese cabbage genomes were added to the system [April. 2013]
*Apple, banana, and watermelon genomes added* -- Apple, banana, and watermelon pathways were added to the system [Nov. 2012]
*Maize genome added* -- Maize pathways were added to the system [May 2012]
*Papaya genome added* -- Papaya pathways predicted from the genome sequences were added to the system [Jan. 2012]
*Sorghum pathways added* -- Sorghum pathways predicted from the genome sequences were added to the system [Sept. 2010]
*Arabidopsis pathways updated* -- Arabidopsis pathway were updated using the most recent version (7.0) of AraCyc database. Arabidopsis datasets in the database need to be reprocessed. Detail on how to reprocess the dataset... [Aug. 2010]
*New organisms added to Plant MetGenMAP* -- Soybean, Grape and Brachypodium were added to Plant MetGenMAP based on their genome predicted genes [July 2010]
See all the news...

This site is supported by NSF IOS-0501778 and IOS-0923312