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Correct GSEA mislabeling in g:Profiler (web) chapter #33

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hosseinvk merged 1 commit into from
Aug 10, 2026
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Correct GSEA mislabeling in g:Profiler (web) chapter #33

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9 changes: 6 additions & 3 deletions 08-1-gprofiler-web.Rmd
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Expand Up @@ -7,7 +7,7 @@ Throughout the following chapters, each web-based tool is paired with its comman
<!-- ## FEA in [g:Profiler](https://biit.cs.ut.ee/gprofiler/gost) -->
## <a href="https://biit.cs.ut.ee/gprofiler/gost" target="_blank"><img src="images/gp2-logo-new.png" alt="g:Profiler Logo" style="height:35px; vertical-align:middle;"></a>

[gProfiler](https://biit.cs.ut.ee/gprofiler/gost) is known for its integration of numerous species and databases. It supports both ORA and GSEA, enabling users to assess Gene Ontology (GO), biological pathways, regulatory motifs and protein databases. With gProfiler one can
[gProfiler](https://biit.cs.ut.ee/gprofiler/gost) is known for its integration of numerous species and databases. It supports ORA, including an ordered/ranked-list mode, enabling users to assess Gene Ontology (GO), biological pathways, regulatory motifs and protein databases. With gProfiler one can

### Steps to perform ORA in g:Profiler:

Expand Down Expand Up @@ -67,7 +67,10 @@ How is multi-query support implemented in gProfiler?

How can one perform Under Representation Analysis in gProfiler?

### Steps to perform GSEA-style analysis in g:Profiler:
### Steps to use a ranked gene list in g:Profiler:

g:Profiler's "Ordered query" option lets you analyse a ranked gene list, but it does **not** implement the Subramanian et al. 2005 GSEA algorithm covered in the GSEA (web) chapter earlier in the book. Instead, it runs standard ORA (hypergeometric/Fisher's exact test) on a series of prefixes of your ranked list (top 10, top 20, top 50 genes, and so on) and reports whichever prefix gives the strongest enrichment for each term. It does not use a running-sum enrichment score, does not weight genes by the magnitude of their ranking metric, and does not use permutation testing — so treat it as ORA over an incrementally-growing ranked list, not as an alternative implementation of GSEA.

<span style="color:orange;">- Prepare Your Pre-ranked List:</span> Steps to provide a ranked gene list are given [here](degust.html).

<span style="color:orange;">- Input Gene List:</span> Paste your prepared gene list directly into the input box on the g:Profiler web page or upload a file containing your list.
Expand All @@ -82,7 +85,7 @@ How can one perform Under Representation Analysis in gProfiler?

<span style="color:orange;">- Run Query:</span> Same as above.

#### **Challenge:** GSEA with gProfiler {- .challenge}
#### **Challenge:** Ranked-list ORA with gProfiler {- .challenge}
Download the Hallmark gene sets ([h.all.v2024.1.Hs.symbols.gmt](https://www.gsea-msigdb.org/)) from MSigDB and use it as Custom GMT.

<!-- Full path to h.all.v2024.1.Hs.symbols.gmt -->
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