Software Installation:
1) Download and install Cytoscape from http://www.cytoscape.org
2) Cytoscape will be installed in the following folder: "Cytoscape_vx.x.x"
3) Locate LoadKEGG.jar file in "cmyc_kegg_cytoscape_distribution/cytoscape plugin" folder
4) Copy LoadKEGG.jar file to "Cytoscape_vx.x.x/plugins" folder
5) Run Cytoscape
6) A "LoadKEGG" option should appear in the "Plugin" menu.
To visualize KEGG pathways and cMyc data:
1) Run Cytoscape
2) From main menu: Plugins -> LoadKEGG
3) Select .sif file for KEGG pathway of interest (e.g. "cmyc_kegg_cytoscape_distributionKEGG/rno00010.sif")
4) From main menu: File -> Import -> Vizmap Property File...
5) Select kegg_vizmap.props in the "cmyc_kegg_cytoscape_distribution/KEGG" folder
6) From main menu: File -> Import -> Node Attributes
7) Select clusters_max9.noa "cmyc_kegg_cytoscape_distribution/KEGG" folder
Notes:
1) File legend.pdf contains information about: colors and clusters, shapes and type of molecules and interactions.
2) File KEGG_metabolims.html shows the correspondence between KEGG ids and pathway names.
3) File clusters_max9.png shows the clusters used to generate the cityscape representation