Now that I have a list of terms that show some significance, I want to figure out how to visualize the data in an informative way. I’m doing some research on gene enrichment visualization tools. Here are some that I’ve come across:
- REVIGO
- The only two processes that weren’t significant were
- negative regulation of biological process
- regulation of anatomical structure size
- I also saved the results in the table REVIGO produces.
- The only two processes that weren’t significant were
-
- WebGivi
- This is a quick example of a visualization that WebGivi does. It might be interesting to reorganize the data such that proteins are drawn to parent terms (rather than GO IDs being drawn to the GO term).
- InterMineR– github here and bioconductor
- Both an enrichment and visualization package in R
- Panther and Gorilla seem to be for model organisms or else you need protein sequences to analyze against the database.
- This website has a list of gene enrichment tools that I want to go through. I’ve come across and mentioned some already, but there is quite a few on here.
- Some good info on gene enrichment interpretation and presentation.
- WebGivi
Additionally, I’m reviewing literature on how gene enrichment has been visualized before, and if there are other methods that might be suitable for my data set.
