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?