Kaitlyn’s notebook: reviewing material for possible next steps or gene enrichment visualization

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.

• • 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.

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.