Detect leaderless proteins from a genes/proteins list

Question

[jose.wo]

Hello all,

I have a list of differentially expressed genes from a proteomic analysis of the secreted fraction of cells in culture. My supervisor has manually curated a list of genes which don't have a peptide signal and others that have it.

I was wondering if I could do this unbiased. I went trough GO terms but I couldn't find the relevant category. Is there any database (ideally accessible with a R/Biocondcutor package) that I could use to label proteins/genes that have/don't have the signal peptide driving their synthesis in the RER??

Best regards and ++ for teleworking in the mist of covid2019!!!

Jose.

Answer 1

[vkkodali_ncbi]

I am not sure which species you are interested in. The following queries apply to human.

RefSeq: use the query Homo sapiens[Organism] AND "sig peptide"[Feature key] AND RefSeq[Filter] in the NCBI Protein portal. You can use REntrez in R with esearch and provide the same query.

Uniprot: use the query annotation:(type:signal) AND organism:"Homo sapiens (Human) [9606]" in UniProt. UniProt has a REST API but I don't know about an R package.

Answer 2

[jose.wo]

Thanks a lot vkkodali!! I'm trying your suggestion now.