I have found the Differentially expressed genes between breast cancer datasets using DESeq2 further I want to find the secreted protein tags for my Differentially expressed genes (DEGs) list. Does anyone have any idea about what tool or database I can use to accomplish this? Please let me know.
Thank you in advance!
•
written
by
koushikayaluri •
you can run some kind of signal peptide prediction tool eg. SignalP or Phobius or DeepSig or, alternatively, if you are working on a well characterized protein set (eg. human) look that info up from for instance UniProt or Ensembl or such.
So to be sure I need to get the fasta sequence of each gene in my Gene list and then I can find the signal peptides?
yes, exactly.
unless you go for the alternative route, then you likely need to collect the (official) geneIDs and query those in one of the public repos.
Thank you! sure will check it.
You can upload your list of genes or other identifiers to the UniProt IDmapping tool and map to UniProtKB at https://www.uniprot.org/uploadlists
Once you have your results, you can click on "Advanced" to the right of the query box and restrict the results to proteins that have a signal sequence annotated (predicted or experimentally determined). This will add "annotation:(type:signal)" to your query.
You may add a column for "Signal peptide" to your result table by clicking on "Columns". This returns data in the following form https://www.uniprot.org/uniprot/?query=annotation%3A(type%3Asignal)&columns=id%2Centry%20name%2Creviewed%2Cgenes%2Cfeature(SIGNAL)&sort=score
which can be downloaded in tab-delimited format.
If you want to download the signal peptides themselves, you can proceed as described here https://www.uniprot.org/help/download_subsequences and replace "domain" by "signal" in these instructions.
Please don't hesitate to contact the UniProt helpdesk if you have any questions about the above.
Log in to answer this question.
What is a secreted protein tag?
I mean to find the signal peptides from my gene list.