From d62a525298e0942013ccf754e72015cbfca6e7d5 Mon Sep 17 00:00:00 2001
From: clbenoit <benoitclement.sand@gmail.com>
Date: Wed, 7 Feb 2024 14:54:23 +0100
Subject: [PATCH] GSEA article edition

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diff --git a/docs/pages/blog/gsea.mdx b/docs/pages/blog/gsea.mdx
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 ## Why GSEA Analysis ?
 
-Genome wide expression analysis has become become a mainstay of genomics research. However, there is still a wide range of tools for interpreting these gene expression profiles. They all have their advantages and disadvantages, and are still evolving. This, coupled with the fact that these studies rely on the testing of a large number of hypotheses and relatively small sample sizes, lead that whole-genome expression studies in particular, to be often not reproducible. 
-This is why reproducibility is one of the major challenges facing studies involving  whole-genome expression data. [^1], [^2], [^3]
+Genome wide expression analysis has become become a mainstay of genomics research. However, there is still a wide range of tools for interpreting these gene expression profiles. 
+They all have pros, cons, and are still evolving. This, coupled with the fact that these studies rely on the testing of a large number of hypotheses and relatively small sample sizes, lead that whole-genome expression studies in particular, to be often not reproducible. 
+This is why reproducibility is one of the major challenges facing studies involving whole-genome expression data. [^1], [^2], [^3]
 
 Finally, interpreting lists of thousands of differentially expressed genes is a tedious exercise for the biologist. 
 
 The GSEA, by dezooming from the scale of the gene to that of the pathway. Improves the reproducibility of studies, while facilitating their interpetation.
 
 ## Principles
- 
+
+### What is the question ?
+
+Let's says you have ranked a gene list <b><i>L</i></b> according to your favourite metric. The GSEA tries to answer the following question : <br/>
+<p className="popacity">
+Given a gene set <b><i>S</i></b> : Does the genes belonging to <b><i>S</i></b> tends to occur toward the top (or the bottom) of the list <b><i>L</i></b>, 
+in which case the gene set is correlated with the phenotypic class distinction.
+</p>
+Of course we will do as many independant tests as we have genes sets to try.
+A [multiple testing correction](https://www.firalis.com/products/fimics-cardiac-ruo-kit-panel) should then be considered.
+
+### The Methods
+
+### To go further
+
+There exists a variant of GSEA called FGSEA for <u>F</u>ast <u>G</u>ene <u>S</u>et <u>E</u>nrichment <u>A</u>nalysis.<br/>
+
+Another common approach to perform pathways analysis is the [Gene Ontology Enrichment analysis](https://geneontology.org/docs/go-enrichment-analysis/).
 
 [^1]:  Timothy E. Sweeney , Winston A. Haynes , Francesco Vallania , John P. Ioannidis
 and Purvesh Khatri. (2017). *Methods to increase reproducibility in differential gene expression via meta-analysis*. **Nucleic Acids Research**, Volume 45(Issue 1), Page Range. [DOI](https://doi.org/10.1093/nar/gkw797)
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