I was wondering if it was possible to access the gene regulation information in KEGG (ie. not just the genes associated with the pathway, but which genes regulate each other also). Is this data available in raw format?
I guess this is what you are looking for,
If you are familiar with Cytoscape (clueGO & cluePedia), you can choose KEGG for enrichment analysis and plot the interactions between genes using BIOGRID option.
Examples:
Supplementary Figure 7, http://www.nature.com/ncomms/2015/150724/ncomms8743/extref/ncomms8743-s1.pdf
Figure 5&7, http://www.cell.com/action/showImagesData?pii=S1535-6108%2814%2900377-8
You can download the KGML. It is an XML file type but designed for explaining KEGG network. In that file, it is defined which gene regulate what gene. The type of the relationship also written there and the explanation of the relationship can be seen in this page. On the other side, KEGG network node is not a gene. It is actually a group of gene. So, two nodes which has relation is actually many to many relationship, not one to one gene relationship. It is written in the KGML what genes are in a node. Unfortunately, you need to write some code to extract this information from KGML. I am actually writing this function right now. Extracting data from KGML into adjacency matrix but it is not yet finished.
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Thank you! Is it possible to access raw text data containing this information from cytoscape. Also when I provide a list of gene IDs it only visualizes which pathways they are associated with and the interactions between the pathways.
You also get plain-text files for complete analysis.