How to identify if a differentially expressed protein is ligand or receptor?

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2.1 years ago

JSPO • 0

Hi All,

I have a list of differentially expressed proteins and would like to know which one of these are either ligands or receptors. How can I identify this?

Appreciate all your help!

Thanks

Proteomics • 984 views

ADD COMMENT • link updated 2.0 years ago by Matthias Zepper 5.0k • written 2.1 years ago by JSPO • 0

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There are many ways, but maybe the easiest for those unfamiliar with programming is the ListAnnotation feature of Intermine. Pick the respective portal for your organism and construct queries based on your list. Possibly, TargetMine will be most useful with regard to ligands and receptors.

ADD REPLY • link 2.1 years ago by Matthias Zepper 5.0k

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Hi @Matthias Zepper,

Thanks so much for the quick response! Are there any R packages you can share which can help me answer the question?

ADD REPLY • link 2.1 years ago by JSPO • 0

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If you are familiar with R or at least prefer a solution in R then please state it specifically in the question the next time ;-) The Portal which I recommended can do similar things in a GUI without writing any code and is thus typically preferred by wet lab biologists.

Your one-stop shop for anything related to bioinformatics in R is Bioconductor. Please find all relevant annotation packages in their handy overview on their page and also see their workflows registry, which are usually very handy step-by-step guides that can be customized as needed.

ADD REPLY • link 2.0 years ago by Matthias Zepper 5.0k

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I think, this is the database right? Can we do from BioMart annotation package also in R and then in that we can also choose for the gene description and type by which we can identify the gene?? please correct me, if i am wrong

ADD REPLY • link 2.1 years ago by qiz218591 ▴ 10

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