How to find the secreted protein tags
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9 months ago

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!

RNA-Seq protein rna-seq R next-gen • 311 views
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What is a secreted protein tag?

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I mean to find the signal peptides from my gene list.

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9 months ago

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.

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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?

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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.

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9 months ago
JC 12k

check SignalP tool

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Thank you! sure will check it.

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9 months ago

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.

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