GO analysis to ID biological processes in my identified protein list? panther? agrigo? (organism is cucumis sativus)

Question

[aronsimko]

Hi Everyone I recently performed total protein extraction from cucumber, digested them and then performed MS/MS. After identifying ~2000 proteins, about 100 are differentially expressed between treatments (infected with pathogen vs not infected). I was hoping to sort what biological processes these proteins are involved in and then further select which proteins to explore in the infection process.

I've been trying to determine which algorithm to use, should I be looking at panther? agrigo? both have support for cucumber. I've read papers where GO output data is then visualized with REVIGO. Is this still currrent? Papers ive read are from 2017 as most recent. Any suggestions for more recent papers, or even tutorials that can simplify this for me so I can have a better background to make better choices here?

[Chirag Parsania]

ClusterProfiler is one of my favourite.

[aronsimko]

Hi Chirag,

thanks for this, ill give it a read through now