I grouped proteins that had 0 abundance on day 1 based on the number of days they were abundant and ran it through CompGO for biological processes at 0.1. To see if there was a differences in the number of proteins expressed in each group, I made a small table. All values were similar. Highlighted values had p-values of at least 0.1.
I think it’s interesting that all silos had enrichment with proteins that had abundance for only 1 day. All silos had peptidyl-tyrosine-dephosphorylation or “the removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine” at p-values greater than 1E-1.
Silo 2- 1 day of protein abundance:
Silo 3- 1 day of protein abundance:
Silo 9- 1 day of protein abundance:
Other enriched processes are:
Silo 2- cellular response to retionoic acid (6 days),
Silo 3- intracellular protein transport (4 days) and maturation of SSU-rRNA from tricistronic rRNA transript (5 days),
and Silo 9: negative regulation of endopeptidase activity (7 days). This can be viewed below in respective order.
Silo 2- 6 days of protein abundance:
Silo 3- 4 and 5 days of protein abundance respectively:
Silo 9- 7 days of protein abundance:
Roberts Lab 