Differences in protein expression between Day 3 and Day 5
In this post I am seeking to understand the differences in protein expression exhibited by all silos between Day 3 and Day 5. In these earlier development stages all silos seem to cluster closely together on each day so I decided to treat all silos as “biological replicates” for Day 3 and compare to the same replicates at Day 5. By asking these questions we should be able to uncover important proteins that oysters are expressing during the settlement phase.
I followed a similar protocol as discussed here.
The file I submitted to Qspec:
The output file
Then I kept all proteins detected with a Z-statistic with absolute value above 2 and a log fold change with absolute value above 0.5.
I split the file and seperated the proteins highly expressed at Day 3 from the proteins highly expressed at Day 5.
Day 3 Highly expressed proteins
Day 5 Highly expressed proteins
I uploaded the annotated files to Galaxy and unfolded the GO column.
Here are Revigo visualizations
High protein expression at Day 3 for all silos
High protein expression at Day 5 for all silos