That being said, the colours used in GeneMANIA were not chosen arbitrarily. We chose the colours of most of the networks to be strong, and we chose much lighter, less saturated colours for co-expression and co-localisation networks.
Often, edges for co-expression and co-localisation form close to the complete graph. Since this does not add much visual information, we decided to make these edges less visually prominent and not affect the layout.
In future, we may have a feature to allow the user to change the network colours. However, this will need to take into account the impact it will have on usability and layout.
In the meanwhile, you can edit the colours of the network in the PDF report with a tool like Adobe Illustrator. The next version of GeneMANIA will support exporting the network as SVG. Since SVG is an open format, it should be easier to edit.