module membership (kME) versus NES (normalized enrichment score) from GSEA
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24 months ago
anamaria ▴ 140


I would like to reproduce fig 4A for my data from this paper: In Supplemental Materials in GWAS Enrichment section they say: "To quantify enrichment of GWAS signal within eachgene co-expression module, we calculated Spearman’s correlation between the module membership (kME) of each gene and the –log10p-value for that gene for each GWAS study. kME is a measure between 0 and 1 of the centrality of a gene within a module; “hub genes” have kME values approaching 1, whereas genes that are not present in a module generally have kME less than 0.5. This process was performed for all module x GWAS combinations, and p values were FDR-corrected."

I did run GSEA analysis and I am wondering is enrichment score from GSEA a reasonable substitute the module membership (kME)?

I can tell you a little bit more about what I am trying to do. So the hypothesis is: Cases versus Controls GSEA pathways are enriched for genes that harbor variants implicated through genetic association Subjects: our meta-GWAS Experiment is: Assess for pathway enrichment from meta-GWAS - do a pathways-based analysis looking for enrichment between the meta-GWAS and the gene expression chip-based data of the transcriptomes cases v controls.

If something obvious is here and can be implemented in analysis design and related to teh above mentioned graph please advise.

Thank you in advance!

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