@@ -41,7 +41,7 @@ Details are provided in the script: [DGE.R](http://www.bioinfotiget.it/gitlab/cu
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@@ -41,7 +41,7 @@ Details are provided in the script: [DGE.R](http://www.bioinfotiget.it/gitlab/cu
6. Dowstream functional Analysis with [ClusterProfiler](https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html).
6. Dowstream functional Analysis with [ClusterProfiler](https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html).
In order to retrieve functional annotation from DE analysis, we performed **O**ver **R**epresentation **A**nalysis and **G**ene **S**et **E**nrichment **A**nalysis by using the functions provided by the package.
In order to retrieve functional annotation from DE analysis, we performed **O**ver **R**epresentation **A**nalysis and **G**ene **S**et **E**nrichment **A**nalysis by using the functions provided by the package.
**ORA** analysis was performed in particular on Gene Ontology Terms (Biological Process sub-group) retrieved by the function.
**ORA** analysis was performed in particular on Gene Ontology Terms (Biological Process sub-group) retrieved by the function.
**GSEA** analysis was performed against MSigDB gene sets C1 to C6 + Hallmarks.
**GSEA** analysis was performed against MSigDB gene sets C1 to C6 + Hallmarks and Senescence signatures (*.gmt files)
Details are provided in the script: [Fig5F_processing_and_plot.R](http://www.bioinfotiget.it/gitlab/custom/zonari_mpbhscexp_2025/zonari_mpbhscexp_2025_bulkrnaseq/-/blob/main/Fig5F_processing_and_plot.R)
Details are provided in the script: [Fig5F_processing_and_plot.R](http://www.bioinfotiget.it/gitlab/custom/zonari_mpbhscexp_2025/zonari_mpbhscexp_2025_bulkrnaseq/-/blob/main/Fig5F_processing_and_plot.R)
