Phenotype Labeling

[AvnS]

I'm attempting to run a GSEA analysis on 9 samples (5 control, 4 mutant). I came upon the phenotype selection and chose the source file. However, I am given the option of either "CNTRL vs MUTNT" or "MUTNT VS CNTRL." What is the difference between the two options? I've attached a screenshot for further information. 

Thank you in advance!

[Anthony Castanza]

Hi Avneesh,

The options there just set the direction of the comparison so if you what to do Mutant in the numerator of calculations or in the denominator. It effectively only impacts the sign of the scores. The traditional comparison is MUT vs. CTRL, so the things that are upregulated in the mutant have positive scores (enriched in mutant) and downregulated in the mutant have negative scores (enriched in control).

Let me know if you have any other questions or this still isn't clear

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

On Tue, Jun 4, 2024 at 9:14 AM AvnS <avneeshsar...@gmail.com> wrote:

I'm attempting to run a GSEA analysis on 9 samples (5 control, 4 mutant). I came upon the phenotype selection and chose the source file. However, I am given the option of either "CNTRL vs MUTNT" or "MUTNT VS CNTRL." What is the difference between the two options? I've attached a screenshot for further information. 

Thank you in advance!

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[AvneeshS]

Hey Anthony,

Thank you so much for the info! I have 2 more questions regarding the results of the Leading Edge Analysis. 

1. What do the numbers resulting from LEA correlate to? Is it percentage increased/decreased? 

2. Is there a way to search for specific genes within the results or organize them in another manner than shown in the heatmap? I've included a graph for reference.

[Anthony Castanza]

Hi Avneesh,

I believe that the value there is the ranking metric value for that specific gene.

The leading edge analysis results have an option to save the data underlying all the plots as tables that you should be able to do whatever you like with.

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

To view this discussion on the web visit https://groups.google.com/d/msgid/gsea-help/ca3a2ebf-9323-4ad4-8362-39c9b58af5fbn%40googlegroups.com.