NeAT - KEGG network provider

Obtain organism-specific KEGG networks from KEGG PATHWAY version . Click on help for help.
Web service and interface by Karoline Faust.

1. Input help


Comment on the demonstration example

We demonstrate how the KEGG network provider can be used to filter the KEGG network. KEGG LIGAND contains many problematic entries, such as generic compounds (e.g. C00030, which represents a reduced receptor) and unbalanced or duplicated reactions (see Félix and Valiente, Biomol. Eng. 24, 327-335 (2007), M.G. Poolman et al., IEE Proc.-Syst. Biol. 153, 379-384 (2006) and Ott and Vriend, BMC Bioinformatics 7:517 (2006)). These entries make path finding and pathway inference more difficult. In this demo, we will construct the reference KEGG RPAIR network, from which we will remove a selection of generic compounds.
Enter full species names as given in KEGG or KEGG abbreviations for organisms, separated by '/' in text field below.
Example 1: eco/ecp/ecs
Example 2: Aspergillus flavus/Aspergillus niger/afm
Example 3: reference
Click here for the full list of KEGG organism names and abbreviations
AND/OR
Upload a file which contains one organism KEGG identifier by line:

AND/OR
Enter KEGG reaction identifiers, separated by '/' in text field below (e.g. R00015/R00551):
AND/OR
Upload a file which contains one reaction KEGG identifier by line:


2. Options help




Optional: KEGG identifiers of compounds to exclude (separated by '/')
Optional: KEGG identifiers of reactions to exclude (separated by '/')
Optional: RPAIR classes to exclude (separated by '/')


Directed network
RPAIR network   
For the conversion of reactions into reactant pairs, a file assembled from KEGG LIGAND is used, which is available here.
Reaction treatment:
    all reactions reversible                                                           
    keep irreversible reactions (only possible in directed networks!)

Optional: The network is constructed with some default attributes. You can add more attributes by selecting them from the menus below, but be aware that this will slow down the network construction. Note also that you can select more than one additional attribute by pushing the Shift key.
Compound attributes
    Reaction/RPAIR attributes



4. Output help



Network format  


Email (optional)

RESET DEMO1 DEMO2 MANUAL TUTORIAL MAIL WSDL