Site Features

Get the data you want in the format you need using the Groups functions at the PMN. 

* Got a list of up-regulated genes?

* Want to know all of the compounds present in the pathways they act in?

* Need to get their structures in SMILES or InChi format?

Then get going with PMN Groups! 

Now you're doubly likely to find Arabidopsis genes using

• AGI locus codes (e.g. AT4G33030)

AND

• Gene symbols (e.g. SQD1)

because the PMN has loaded the latest set of gene "symbols" from TAIR into AraCyc. 

Now over 4600 symbols are linked to over 3100 genes!

We hope this will make it easier than ever to find your favorite metabolic genes in AraCyc!

Did you know that you can download all eleven of the PMN databases plus the Pathway Tools software?

Working on a local copy of a database enables you to:

1. Build your own pathways
2. View graphs of Omics data directly on pathway pages
3. Analyze groups of data to find unique and shared elements
4. Create a new database for your favorite species

You can try it out today! 

Use the improved Metabolic Overview to easily

• overlay experimental data
• find and highlight compounds, enzymes, and reactions
• zoom and pan

against the backdrop of the Arabidopsis or Poplar metabolic map! 

Whenever you are viewing a single species database like AraCyc you can access the Metabolic (Cellular) Overview from the Tools menu

• Have you attended a PMN workshop or presentation and wanted to review the material?
• Did you miss a PMN talk at a recent conference and want to catch up?
• Have you been looking for a quick way to find out about the data and tools available in the PMN?
• Then please check out our presentations page and find an array of talks that aim to help researchers and students get access to the plant metabolic information they need.

Are you looking for an enzyme in Arabidopsis or poplar that is similar to your favorite protein? Please check out the two new datasets that are available for BLAST analyses: 

• AraCyc Enzymes
• PoplarCyc Enzymes

Our original Reference Enzymes and PlantCyc Enzymes datasets are also still available for sequence similarity-based searching. 

New viewer for a global metabolic map

• Do you want to highlight a compound or reaction on a global metabolic map for a single species?
• Would you like to overlay your transcript expression, proteomic, or metabolomic data onto a zoomable set of pathways?

Please come check out the new metabolic (cellular) overview using AraCyc or PoplarCyc. 

The PMN is eager to work with scientists who want to do metabolic-pathway-based analyses.
PlantMetabolomics.org is a data repository for a series of metabolomic experiments performed in Arabidopis thaliana
You can read about efforts to incorporate their experimentally identified compounds into AraCyc in Bais et al 2010

Have you ever wondered what information PlantCyc has about apples, bluebells, or carrots? To find out more, please come visit the newly created PlantCyc species page found on the "Databases" submenu.

• Quickly link to all of the pathways with curated information for your favorite species
• Browse through the list of over 250 species, from Abies grandis to Zingiber officinale
• Help the PMN expand its species coverage by contributing pathway, reaction, or enzyme information for even more plants

• Come see new links to metabolite identification resources and data analysis tools from PRIMe on our Metabolomics Resources page.
• While you're there, explore the array of helpful websites you can access through these pages.