Gene function KEGG and GSEA

Question

[loly.pearl86]

Hi everyone,

My question here is about KEGG pathway , 1) When i do DGE to understand the function/role of specific gene and followed by GSEA, Do i still need to perform the KEGG pathway ? or GSEA its enough to identify the gene function ?? 2) I got GSEA results and its iluustrated list of GO terms , the question is how can i know this list of gene related to what ? its for sure one of GO category but i mean :

how can i classify the genes if all of them related to metabolism or immunity response ...etc

Thanks

[GZ1995]

MSigDB has the list of KEGG and GO terms. Personally I prefer GSEA than conventional GO and KEGG fisher test because it is less sensitive to arbitrarily defined cutoff for DGE, but usually two methods would not differ too much. I don't quite understand your second question. What do you mean by classifying the genes ?

[loly.pearl86]

Thanks for your answer.

I mean that the group of gene of GO terms some of them related to protection role in the cell and other reasonable about metabolism ...etc of different function ..so how can i summaries my set of gene, i mean are there any way to do them instead of read and identify them individually ?

thanks

[GZ1995]

Test your set of genes with GO/KEGG/GSEA. If there is an enrichment of your set of genes in specific GO/KEGG terms, then just look at DEGs presented in that category.