How to Intrepret

[Arko Samad]

Upon running an analysis and click on details, below the enrichment plot, I see a list of genes with the following columns: Symbol, title, Rank in gene list, rank metric score, running ES, and core enrichment

What is the best way to interpret this list and is it possible to infer the upregulation/downregulation of a gene based on it

Also, there is a plot beneath the gene list with blue and red squares: what does that represent?

Thanks 

[Anthony Castanza]

Hi Arko,

The plot with red and blue squares is a row normalized heatmap of the expression from your dataset of the genes in the gene set.

GSEA's calculations are not intended to determine individual significant genes, single gene changes are better calculated with a specialized tool such as DESeq2 (in fact, standard normalization pipelines intended to get RNA-seq data into GSEA suitable forms commonly involve extracting the normalized counts matrix from tools like DESeq2 in parallel with computing standard differential expression). GSEA's intent is to determine if groups of genes  are collectively differentially expressed based on their overall distributions within the full expression data.

Have you read through the user guide section on interpreting GSEA results?
The section here: https://docs.gsea-msigdb.org/#GSEA/GSEA_User_Guide/#interpreting-gsea-results describes the mountain plots and some of the other important plots with annotated diagrams.

Let me know if you have any other questions after reviewing this

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

--
You received this message because you are subscribed to the Google Groups "gsea-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to gsea-help+...@googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/gsea-help/7b154c4a-d653-410f-8621-3c90baf613d9n%40googlegroups.com.