We can get the elements (genes) of each pathway of KEGG from KEGG website of UCSC database. However, how can we get the network relationship in the form of network for KEGG pathway as the following figure?
Suppose I have a network, I want to find the similarity between my network and KEGG pathway network. Therefore, I need the mathematics form of KEGG pathway.
Best regards,
Hi Shicheng,
Generally there are some difficulties in reconstructing KEGG maps using due to restricted accessability to the language used to construct them.
In case you have not seen it, I would recommend you the following paper:
"Rebuilding KEGG Maps: Algorithms and Benefits"
http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6787142
Ilian
Can not see the figure, and unclear about mathematical form?
You can simply map you gene/protein list to KEGG pathway via online "User data mapping" function of KEGG itself or other bioinformatics tools (such as DAVID or webgestalt). Or you can download the KEGG file (http://www.kegg.jp/kegg/download/) and handle it with your local scripts.
Alternatively, you can use wikipathway which provides GPML (Graphical Pathway Markup Language) format and simple tab-delimited file. You can check http://www.wikipathways.org/index.php/Download_Pathways to find a favorable format.
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