Classify, organize, and cluster a list of proteins / discovering relations between a set of proteins and linking them to disease

Question

[']

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 R packages or databases that will let me do this comprehensively?

[GenoMax]

their names only

What kind of names? Since there is no standard nomenclature this would become an herculean task unless you have some specific needs (standard identifiers (e.g. uniprot) of a certain kind, specific organism).

[']

Fixed now. It was a mistake.

[Pierre Lindenbaum]

give us a few examples of Uniprot IDs please

[']

"P06909", "Q3UV17", "P07724", "Q61147", "Q6ZPJ3", "P20918", "Q7TT37", "Q62469"

[microfuge]

Simplest would be to put the ids in string database , presumably if they belong to same species.

[cpad0112]

try reactome also@OP . Proteins seem to be from Mus musculus.

[GenoMax]

This is the critical requirement. So a functional consequence differential analysis between two networks.

I have two lists for two groups, and I want to know if the expression of these proteins in one group and absence in the other indicates any biological phenomenon (mainly disease-related, but as mentioned any other 'classification' can be helpful too).

Answer 1

[Pierre Lindenbaum]

use the uniprot SPARQL Graph to find some relationships between your proteins. I've played a few minutes with it, but I cannot find anything with the example provided (output dataset is empty). https://sparql.uniprot.org/sparql/

PREFIX up:<http://purl.uniprot.org/core/> 
PREFIX taxon:<http://purl.uniprot.org/taxonomy/> 
PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#> 
PREFIX skos:<http://www.w3.org/2004/02/skos/core#> 
SELECT ?p1 ?p2 ?annotation ?text
WHERE
{
        ?p1 a up:Protein . 
        ?p2 a up:Protein . 
        ?p1 up:annotation ?annotation .
        ?p2 up:annotation ?annotation .
        ?annotation rdfs:comment ?text .


         FILTER (?p1 IN (<http://purl.uniprot.org/uniprot/P06909>, <http://purl.uniprot.org/uniprot/Q3UV17>, <http://purl.uniprot.org/uniprot/P07724>, <http://purl.uniprot.org/uniprot/Q61147>, <http://purl.uniprot.org/uniprot/Q6ZPJ3>, <http://purl.uniprot.org/uniprot/P20918>, <http://purl.uniprot.org/uniprot/Q7TT37>, <http://purl.uniprot.org/uniprot/Q62469> ) ).
         FILTER (?p2 IN (<http://purl.uniprot.org/uniprot/P06909>, <http://purl.uniprot.org/uniprot/Q3UV17>, <http://purl.uniprot.org/uniprot/P07724>, <http://purl.uniprot.org/uniprot/Q61147>, <http://purl.uniprot.org/uniprot/Q6ZPJ3>, <http://purl.uniprot.org/uniprot/P20918>, <http://purl.uniprot.org/uniprot/Q7TT37>, <http://purl.uniprot.org/uniprot/Q62469> ) ).
         FILTER( STR(?p1) < STR(?p2))
}