More tables for 2015 _C. gigas_ seed

Today I spoke with Steven about what the results are for the 2015 C. gigas seed paper. I made a new annotated table for the 69 differentially abundant (though not significantly) proteins. Edits to paper.

Annotated table of 60 diff. expressed proteins

I used the proteins_comp_annot_threshold.csv which was made a few days ago from Steven’s annotated list, with a set threshold of 2.00 and -2.00 log-2 fold changes.

I did this in jupyter and R:
01-blastp-to-GOslim.ipynb (to get GOslim terms for the BLASTp results from Steven)
02-detected-prots-annotate-GOslim.ipynb (to get the protein list into a good format with just the columns we want)
04-join-annotate-diffexp-prot.R (to join the GOslim with the protein list)

The final file: diffexp-prot-annotated.tab
Not super sure why there are so many proteins… I was only expecting to annotate the 69 differentially expressed. I’ll have to fix that.

Paper updates

paper
Worked more on edits and clarifications.

Results that I’ll aim to have:
Phenotype:

  • condense to a few sentences (no graphs)

Proteomics:

  • MS Stats (not sure if should have as supplemental, or if I should include some in paper)
  • Protein list from MS stats (annotated - GO)
  • Protein list of the 69 diff abundant (annotated - GO)
  • Maybe a visual (REVIGO?)
Written on April 9, 2019