What happened at Day 9?
04/30/2017
Day 1: Black, Day 3: Red, Day 5: Orange, Day 7: Yellow, Day 9: Green, Day 11: Blue, Day 13: Purple, Day 15: Magenta
In the NMDS plot we noticed a divergence occuring at Day 9 between all of the silos. Here I compared Sample 27 (Silo 223C at Day 9) with 32 (Silo 929C at Day 9). See table
I used Qspec to calculate statistics:

First using Qspec I calculated statistics associated with differential protein expression between Silo 223C and Silo 929C at Day 9. Here is the file

You will get an output with Z statistics and log fold change values. You want to consider all proteins with a Zstatistic with absolute value of at least 2 and a log fold change with an absolute value of at least 0.5.

Next you will annotate this file by joining (I like to use Galaxy). Here is the file I used to join with my output file from Qspec.

After annotation I sorted the file using true values. The negative values represent highly expressed proteins in your “0” treatment or your first column in the file you uploaded to Qspec. The positive values represent highly expressed proteins in your “1” treatment or second column.

Then I seperated the file into two files one with proteins highly expressed in my Silo 223C and one with proteins highly expressed in Silo 929C.

Now for each file, I sorted to remove any proteins that did not fit the statistical criteria described above.

I uploaded these two files in Galaxy and unfolded the GO column.
 Here are my two files:

Next I copied and pasted the GO terms and the associated Zstatistic to a new sheet. There were some proteins that were not annotated and so I deleted if there was no GO term associated with it for the Revigo analysis.

Here are the Revigo visualizations