GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
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danalvoronov ▴ 10
Last seen 9 weeks ago


I am trying to figure out the meaning of the results of gage analysis when input is gene Entrez ID in row names and the column is the fold change ranging from negative to positive.

What confuses me is the meaning of "greater" and "less". I know in other answers the authors say that it refers to up or down regulated pathways, but this is unclear to me and the documentation is unclear either. Does up or downregulated pathways here refer to genes from pathways and those genes have positive ("greater") or negative fold change ("less")? Or does it deal with upregulated pathways in the sense of more or less genes involved, like over-representation analysis?

If it is the former then I do not understand how I get "greater" and "less" in cases where I subset my input to only have negative fold change? Where does the greater come from then? If it does not work like that, then what is the cut off where the software, in the list of ranked genes (by foldchange), determines a pathway as upregulated.

Is the interpretation of results same for gage run for KEGG and GO?


Best, Dani

GO KEGG gage pathview • 126 views

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