Question: Constructing Enzyme Network
gravatar for Woa
8.1 years ago by
United States
Woa2.8k wrote:

I wish to construct an Enzyme network, where two enzymes would share an edge, if the product(small molecule) of one enzyme is used as a reactant for the other enzyme.

I've a couple of hundreds of such enzymes for an organism, and I know their EC numbers. Can somebody provide a brief guidance about where to start from? Can the API of KEGG be used? If so, can one cite a small example?

Thanks in advance


network kegg enzyme • 2.2k views
ADD COMMENTlink modified 8.1 years ago by Alex Paciorkowski3.4k • written 8.1 years ago by Woa2.8k
gravatar for Alex Paciorkowski
8.1 years ago by
Rochester, NY USA
Alex Paciorkowski3.4k wrote:

You can use Cytoscape to do this. If you have a tab-delimited text file with the following information:

EC     shares_reactant_with       EC

You can then import the file into Cytoscape, select the select the columns "source interaction" for column 1, "interaction type" for column 2, and "target interaction" for column 3. This will draw a network, which you can modify using Cytoscape's layout options. Is this what you are after?

ADD COMMENTlink modified 10 months ago by RamRS30k • written 8.1 years ago by Alex Paciorkowski3.4k

Thanks Alex, but I need to establish the edge relationship first. I just have a collection of nodes(enzymes) with the EC numbers. I need to know which reaction they catalyze, and based on that info. I have to tell whether they can have an edge between them. Their can be some potential glitches. Common co-factors like FAD, ATP,ADP etc. I think should be excluded and enzymes separated in subcellular compartments where they have least chance to react should be excluded. Anyway that sort of refinement comes second to finding out the catalyzed reaction, the reactants and products.

ADD REPLYlink written 8.1 years ago by Woa2.8k

Then I would recommend using a structured ontology like KEGG's BRITE hierarchy, that will allow you to identify (and exclude) the common co-factors you mention.

I'm not sure however whether all of your enzymes are represented in the hierarchy.

ADD REPLYlink written 8.1 years ago by Alex Paciorkowski3.4k
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