Using two tools, I want to run an enrichment analysis on differentially expressed genes post-DEseq2 from a bulk RNAseq experiment. I plan to use Metascape and gProfiler.
gProfiler has the option to input ordered or unordered gene lists. I am not sure if the same can be done in Metascape.
Also, I am pretty new to this analysis and not sure under what criteria/conditions can the genes be ordered. Any suggestions and recommendations for other bioinformatic tools are appreciated!
Junbo Yang
The main statistical test for pathway enrichment analysis is the hypergeometric test. This test is not sensitive to the gene list order. I suppose you are doing GSEA analysis when you use an ordered gene list.
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