Laura’s Notebook: An alternative look at proteins

Following up on my Proteins of Interest, Part II analysis, I am taking a second, simpler look at the peak area data. This time, I am simply taking the total peak area for each protein and averaging across each treatment:

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Then, using Galaxy, join the proteins that are up/down regulated by 5x with the annotations:

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Added column names:

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And counted the number of proteins in this list, which is 76. This file is found in the DNR_Geoduck repo

Then, using Galaxy I joined my two datasets to identify which proteins were found to be diff. expressed in both the treatment/site analysis and the treatment-only analysis. Using Revigo I did a quick visualization:

Expressed more in Bare patches:

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Expressed more in Eelgrass patches:

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