I have about 200 differentially expressed genes. How should I know which genes make the secreted protein?
Short answer: unless the function of the genes is already known, you can't learn this from RNAseq.
Wouldn't it be possible to screen for export signals in the translated peptide sequences? Certainly not the most promising approach (which is why I would use annotations where available), but a viable alternative - or am I missing something here?
Sure, but my point was really that that's a waste of RNAseq when you could just do that from a genome annotation as you mention.
I think a better approach would be to use this for pathway enrichment and interrogate which pathways are associated with secretion?
Is your organism annotated? In that case, see for example this and this response.
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