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.
In RNA-seq (which I can comment on since I am not a protein guy) you'd take the gene names of the differential genes and submit them to pathway enrichment analysis, e.g. with ClusterProfiler, gProgiler, EnrichR and similar tools. I guess if you have differential proteins (abundances I guess?) then you can do the same, so get the gene names and see which pathways are involved with the above mentioned tools.
Thank you for the response. May I ask, I a new on using R.
May you please suggest me a good example for an R pipeline I can use from installing R packages to loading the dataset and comparing the enrichment profiles on ClusterProfiler.
It will be nice to have some suggestions or general codes to use.
The manuals of the tools contain example code. gProfiler and EnrichR are also available as web-versions.
Thank you very much, I will try the manual then. gProfiler and EnrichR web version seem to be not having E.coli database if I am not mistaken.