Question: Help interpreting a published figure that mixes GSEA and KEGG pathway analysis
gravatar for JP
4.4 years ago by
JP0 wrote:


I was reading a recent paper ( and am struggling with one of the figures. Specifically, Figure 1A states:

(A) GSEA demonstrates up- and down-regulated signaling pathways in MuSCs from 2-year-old mice, as compared with 3-month-old mice. This panel shows the results of our analysis of microarray data from the publicly available GEO data set (accession number GSE47177), using Kyoto encyclopedia of genes and genomes (KEGG) enrichment. Signaling pathways were ranked on the basis of normalized enrichment scores (NESs); positive and negative NESs indicate down- or up-regulation, respectively, in aged MuSCs. Specific pathways related to MuSC function are highlighted in red and blue. TGFβ, transforming growth factor–β Figure 1A

What does the horizontal scale represent? Is it simply some arbitrary unit? Is it some kind of measure of KEGG signaling pathway matching?

How would one go about generating such a figure? Perhaps that would best explain how to interpret this panel...

Thanks! JP

gsea kegg • 3.0k views
ADD COMMENTlink modified 4.3 years ago by Biostar ♦♦ 20 • written 4.4 years ago by JP0

I believe the horizontal axis to be just the rank of the pathway, i., "Cytokine/receptor" is the pathway with lowest NES.

I do not think that the figure is explanatory and thus, you should not try to reproduce it. However, if you really want to, you can

  1. Do GSEA
  2. Select 50 pathways starting with the one with the highest NES and plot rank vs. NES
  3. Select 50 pathways starting with the one with the lowest NES and plot rank vs. NES on the same axis.

EDIT: If you believe, that you should be able to understand that article because you know things like GSEA, KEGG, etc. you should ask the authors of that paper why they presented the data in this way. It is the job of every author to explain their findings in a way which allows reasonably educated people to reproduce the results. Probably they missed that point here... ;-)

ADD REPLYlink modified 4.4 years ago • written 4.4 years ago by Manuel Landesfeind1.3k

Thanks for your response. It is somewhat a relief to hear someone else's view that this is not a terribly useful figure. I think that you are right, that I won't try to reproduce this. There must be better ways to communicate this information. Then again, perhaps it all made sense at some point in time, but reviewers and editors had their say and things got changed around and shortened...

ADD REPLYlink written 4.4 years ago by JP0
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