Dear community, i have knockout mouse and performed total RNA seq analysis comparing knockout with wildtype mice. Now I have a list of about 13000 genes. There is an inhibitor of this protein and it was used in patients. Authors also performed RNA seq analysis and published a list of genes, which are differentially expressed under treatment of this inhibitor. To compare published Data with my transcriptomic data i decided to use GSEA. I have seen several publications perfoming such analysis. So i transform published human genes to mouse orthologs, make ranking of my 13000 genes and performed preranked GSEA analysis. GSEA analysis showed that both gene sets are enriched with NES 1.4 for upregulated genes and NES -1.37 for downregulated genes, both with FDR < 0.05, that i can say that transcriptomic data in humans under inhibitor treatment and in knockout mice are comparable. Now i got a lot of critic about the analysis, that i can not use it for this purpose. My question is it okay to perform such kind of analysis? As i understand the original GSEA Paper this analysis was developed exactly for such things. I also search this Forum and GSEA was also recommended for such analysis.
Question: Using of GSEA to compare RNA seq data with published gene sets?
7 months ago by
Fedo • 0
Germany / Cologne / CECAD
Fedo • 0 wrote:
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