Oysterseed DIA - trying to characterize list of detected proteins in relation to _C. gigas_ proteome

I’m still working on wrapping up the results and discussion of this paper. Steven recommended I look into characterizing the list of detected proteins (2,808) in relation to the whole C. gigas proteome. Detailed in post:

DAVID (from 9/27/19 post)

Gene list: Uniprot accession #s from 2,808 detected proteins –> Cgseed-protcomp-annotation-name.sorted
Background: Uniprot accession #s from C. gigas proteome –> 0327-cgseedblast-sprot.tab

Resulting file: david-diffex-proteome.txt

Excel to pare down DAVID results:

Steven recommended only looking at DAVID GO IDs that had <0.05 FDR.
New list –> 108 GO IDs

REViGO

I put the 108 GO IDs and their respective fold enrichment values into REViGO (0.7 allowed similarity; numbers associated with GO terms are other than -pvalues, where larger is better) and got the following:

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I put them in the paper in the results section and basically said that the most enriched GO processes were to do with general functioning and growth…

Paper writing:

I’ve been woring on clarifying things in the Methods, and working on the discussion. All still very much “work in progress”.

Written on September 30, 2019