I am doing proteomic analysis, and I want to compare the function of scored proteins IDs that are significantly expressed. I want to compare and assess differences between these protein IDs for E coli-Wild type and E coli-Knockout strains based on the biological, cellular and molecular function.
Suppose I have 100 protein IDs for wild type Ecoli and I have 100 proteins IDs Ecoli (with a knockout in a specific gene), what tool or package can I use to generate a graphical plot showing differences between them based on on the biological, cellular and molecular function in one graph for example.
It will be nice to know some suggestions on the steps I can use or do as I am not still in my infancy with my bioinformatics knowledge.
Thank you :), I hope for some positive helpful feedback. Have an awesome day.