Using the Metabolic Map / Cellular Overview Diagram
The Metabolic Map Overview provides a bird's eye view of all of the pathways in a given species
  • Therefore it can NOT be used with multi-species databases such as PlantCyc.

On the Metabolic Map Overview the pathways are represented by schematic illustrations and provide an entry point for browsing data in a database.
  • The pathway overview diagram also forms the basis for the Omics viewer which is used for overlaying expression, metabolomic and proteomic data onto biochemical pathways.
    (See the OMICS viewer tutorial)

Accessing the Metabolic Map / Cellular Overview diagram

There are two ways to access the Metabolic Map Overview of the database for each species:

  1. From any page go to the menu bar:
    - Select Databases -> Metabolic Map and choose the database of interest from the drop-down menu

  2. From the Query page select the organism of interest using the Select a dataset drop-down menu and then click on the Cellular Overview:"Diagram" link found halfway down the page.

Understanding the Metabolic Map / Cellular Overview diagram

The overview diagram shows all of the pathways that are included in the database.

Pathways are arranged in the diagram into various loose groupings:
  • Catabolic processes (right side)
  • Anabolic/biosynthetic pathways (center)
  • Intermediary metabolism (left)
  • Reactions that are currently not assigned to any pathway (extreme right).
  • Signal transduction pathways (if they are entered) (bottom)
  • Transporters (if they are entered) (periphery - crossing the border)

To distinguish elements in the overview diagram, a key is provided in the upper right hand corner.

Pointing the mouse over any of these elements will display a pop up window.
  • On mouse-over, the name of compound, pathway, and when available, the super pathway are displayed.
  • Click the mouse and the pop up expands and displays hyperlinks to the various elements. In addition it also shows the genes for each reaction.

There is no way to perform a text search for a compound, enzyme, etc., in a web browser.

**** These search features ARE available if you download and install the Pathway Tools software and download and create a local copy of the species-specific databases

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Please contact us if you have any questions or check our FAQs page for answers to common questions.


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