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I came across this paper as one of the examples from this paper, this one

Figure 2. Host Protein Alterations in Infected iAT2s

(B) Dysregulated (FDR < 0.05) functional modules, including (bottom) U7 snRNA and HDAC-associated complexes.

So how should be the data frame should be for my clustering and visualization. If i have to replicate the same for lets say 4 different time point how to do that.What i have done so far.

I have 4 condition C1,C2,C3,C4. I did pairwise comparison between C1vC2, C2vC3 , C3vC4.

So now I did pathway enrichment with the comparison above. I have for C1vC2, then C2vC3 and C3vC4.

Now I how to proceed what they have shown here. Do i intersect all the pathway that is common in all three? such that based on the any metric that is present I can cluster and show the differences or is there any simpler way.

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