I have a list of proteins (only
Uniprot IDs) and I am interested in discovering relations between them.
Most importantly I want to focus on disease pathways and find out whether the proteins I am looking at are part of particular disease(s). Additionally, functional relations, pathway analysis, simple category/class of protein, etc. can be helpful too. But disease pathways are the most important analysis for me.
I have two groups of patients and the proteins of interest are absent in one and present in the other. As an example:
PROTEIN GROUP1 GROUP2 Q64511 1 0 Q01320 1 1 Q8CIZ8 1 0 Q60865 0 1 Q8VDP4 0 1 P80318 1 0 Q3TXS7 0 1
0 = protein of interest is absent in the group
1 = protein is expressed
Are there any suitable Bioconductor/R packages for this purpose?