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:
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”.