I have continued working with Rhonda’s data and did some gene enrichment analysis on any proteins that had abundance on any day of the experiment after 0 abundance on day 1. I used Animal Genome for GO terms and produced a graph based on those GO terms.
I also made a graph for GO terms that had 0 abundance on any day of the experiment after some abundance on day 1.
I also thought it would be worthwhile examining what process seemed to change overall. Therefore I combined the data and produced the following graph:
Although biological process isn’t descriptive, for many proteins that was the only GO term which can be seen in screenshots and charts here. Furthermore, of the proteins I identified, many were not enriched which is why I choose to analyze gene enrichment for proteins that appeared or disappeared at any point in the experiment.
However I have now produced excel sheets that can identify proteins that were expressed only 1, 2, 3, 4 or all 5 days after no abundance on the first day. In other words we can now look at proteins based on the number of days they appeared after 0 abundance. This is also separated by silo as the analysis was before.
You can see that the original data was converted to a dichotomy using R and then based on the sum of those columns, we can identify proteins that were abundant for 1, 2 , 3, 4 or all 5 days. I included the original data so that we could identify if any of those proteins were abundant at very high levels such as the protein in the second photo that was expressed on only 1 day but at almost 40 abundance. I also included some annotations that we can look through as well.
Here are the links for the other silos: