Hi Veronica,
I’m assuming the 500 genes are considered of interested somehow (differentially expressed?). To find pathways of interest, here are two options:
1. Load your full dataset (not just the 500 genes) into PathVisio (
https://www.pathvisio.org/), and then use the “Statistics” feature (with the WikiPathways archive loaded) to find interesting pathways. For example, if you filtered your dataset based on some parameter (p-value etc) to get the list of 500, you setup the same criteria in the Statistics interface. You can see an example workflow here:
https://www.pathvisio.org/documentation/tutorials/tutorial-2/
2. Use a third-party tool that incorporates WikiPathways content, directly on the list of 500. For example, Enrichr (
http://amp.pharm.mssm.edu/Enrichr/) takes a list of genes and performs over-representation analysis against WikiPathways, GO and many other libraries. Once you have a list of pathways, you can open those in PathVisio, load your data and visualize it on the pathways.
Hope this helps,
Regards,
Kristina