Question: Protein pathway analysis -- Classify, organize, and cluster a list of proteins / discovering relations between a set of proteins and linking them to disease
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16 months ago by
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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?

ADD COMMENTlink modified 16 months ago • written 16 months ago by 0

Check clusterProfiler & DOSE package

ADD REPLYlink modified 15 months ago • written 15 months ago by prakashpandey11110
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