RNA seq, secreted protein
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8 weeks ago
Rob ▴ 160

Hi all, I have about 200 differentially expressed genes. How should I know which genes make the secreted protein?

protein gene secreted • 347 views
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Short answer: unless the function of the genes is already known, you can't learn this from RNAseq.

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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?

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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?

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Is your organism annotated? In that case, see for example this and this response.

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