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meyer-lab / DDMC

Clusters phosphoproteomics data based on a combination of the sequence information and abundance changes over conditions.
https://asmlab.org
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Tentative Interpretation Scheme #429

Closed mcreixell closed 3 years ago

mcreixell commented 3 years ago

@aarmey What do you think about combining the enriched GO processes with a STRING map of the proteins involved in these pathways? This is how it would look like in figure 5. I wanted to ask before doing the same thing with figures 6 and 7.

mcreixell commented 3 years ago

FigureM5

mcreixell commented 3 years ago

Finding a good way of showing what's inside the clusters and proof-reading the text are the last two items I want to take care of before finalizing a first draft of the manuscript and asking for your review.

aarmey commented 3 years ago

What information does the STRING map reveal?

mcreixell commented 3 years ago

It illustrates what molecules are driving these GO processes and their interactions. For instance PEAK1 seems to be a key modulator or link of both Gas/Oxygen transport and cytoskeletal remodeling.

mcreixell commented 3 years ago

In cluster 12, STRING helped me see that CDKs play an important role as well

aarmey commented 3 years ago

Unless there is literature supporting those conclusions I'd be very hesitant to make much of these STRING diagrams. They are heavily biased toward finding connections among highly connected or highly studied proteins.

mcreixell commented 3 years ago

Sounds good, then I will just show the GO enrichment score bar plots.