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How can you establish that only gene symbols are shown instead of enzyme names in Cellular Overview?

asked 2016-03-02 16:16:29 -0500

anonymous user


I need to remove the description of the enzyme (for example, adenylosuccinate lyase: ADSL) in order to show only the gene symbol (ADSL in the example) in the Cellular Overview. I haven't found the way to do it and then save the overview with those abbreviations only. Same applies to metabolites.

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answered 2016-03-03 16:38:06 -0500

Suzanne Paley gravatar image

The GUI doesn't allow you to change it, but there is a parameter that controls whether or not enzyme names are included in the cellular overview. You will need to issue a lisp command in order to change it. One way to do this is via the -eval command-line arg, i.e. invoking pathway-tools with the following command:

pathway-tools -eval '(setf *overview-include-enzymes?* nil)'

Another way is to start up pathway-tools in lisp mode using the provided shortcut or the -lisp command-line arg, and paste the following at the lisp prompt:

(setf *overview-include-enzymes?* nil)


(The second line above just brings up the GUI.) Whichever method you choose, once the GUI appears you will need to regenerate the cellular overview diagram for your organism using the command Overviews->Update. Once the overview has been regenerated, it is automatically saved -- you don't need to execute the above lisp expression next time you restart the software unless you plan to update the overview diagram again. Note that this is not supported functionality and hasn't been fully tested -- I can't guarantee results.

There is currently no analogous parameter to suppress metabolite labels in the cellular overview diagram.

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Asked: 2016-03-02 16:16:29 -0500

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Last updated: Mar 03 '16