what is applications of gene ranking except GSEA?

Question

[Zhilong Jia]

Gene ranking is to ranking all the genes measured by Microarray or RNA-seq. GSEA is one of applications of gene ranking. So what else application of it? Help me list some, please. Thank you.

[Chris Evelo]

Actually I would not say that that is what GSEA is. GSEA (gene set enrichment analysis) ranks sets of genes (typically from pathways or ontology classes) based on the (expression change) values of the genes in these sets. So it ranks the sets not the genes, although it uses the gene ranks to derive the set ranks. An often used alternative for GSEA is a much simpler enrichment score that just calculates an enrichment z-score for all genes in a set meeting a specified criterion (e.g. p -value<0.05 AND fold change >1.5).

Answer 1

[mark.ziemann]

SeqGSEA, GSAA, MRGST, Camera, Roast are some.