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What Is The Best And Most Complete Source Of Secretory Data For Mammalian Genes?

What open resources are the best for annotating genes as being secreted for mammalian genomes (e.g. rat, mouse, human)?

I know EnsEMBL proteins have signalP and TMHMM features which can be queried via EnsMART or SQL, and can query based on GO terms. Uniprot also has annotations for well known genes. What other resources exist that are reliable and easily accessed?

protein gene
• 3,400 views • link
updated by Andrew Su Andrew Su • written by hurfdurf hurfdurf

4 answers

The Secreted protein Database can be downloaded.

NCBI gene?

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updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

Have you tried the methodology used in this recent paper on a prediction method for secretory / non-secretory proteins ? They extracted positive dataset from Uniprot using sub-cellular localization annotations in the comments block.

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updated by Ram Ram • written by Khader Shameer Khader Shameer

[?]

http://locate.imb.uq.edu.au/

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updated by Ram Ram • written by Fred Fleche Fred Fleche

Phobius

Also, this paper (in which I was involved) described a pipeline for defining the set of secreted proteins. I think it's also available as a downloadable file...

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updated by Ram Ram • written by Andrew Su Andrew Su

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