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wangxlab / IndepthPathway

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Difference between feature.list and compare.list #2

Open saneglaz opened 6 months ago

saneglaz commented 6 months ago

Hi, nice work.

I'm trying to use your tool but I don't understand the difference between feature.list and compare.list. Could you explain it?

Additionally, I have seen that you have another version in “biotech25/indepthPathway” (v2.8.5). Which one do you recommend to use?

Thanks

sanghoonleepitt commented 6 months ago

@saneglaz I am sorry for the late response and thank you for your interest in IndepthPathway.

I understand why you are confused between feature.list and compare.list. Probably we could have named them easier to distinguish well. 'feature.list' and 'compare.list' have the same class, "list", in R and many elements of the lists are common, so it is confusing. For example, both of 'feature.list' and 'compare.list' have "HALLMARK" gene signatures.

grep("HALLMARK", names(feature.list), value=TRUE) grep("HALLMARK", names(compare.list), value=TRUE)

Difference between 'feature.list' and 'compare.list' is that 'feature.list' is much more comprehensive and we used it for functional interpretation of a target gene list (weight of genes), and the functional interpretation is represented as uniConSig scores [Materials and methods, section 2.1]

length(feature.list) [1] 21828 length(compare.list) [1] 2547

'compare.list' is used to calculate the pathway enrichments from the uniConSig score of the target genes. Please note that we calculate 'up.uniConSig' and 'down.uniConSig' scores [Materials and methods, section 2.2]. If you are interested in only HALLMARK gene signature enrichment, you can subset only HALLMARK signature from compare.list and run CSEA2( ). If you are interested in DNA repair pathway enrichment, you can subset only those pathways from compare.list and run CSEA2 ( ). For now, we just made a broad compare.list and provide it for users.

MyCompareList <- compare.list[grepl("HALLMARK", names(compare.list))] names(MyCompareList)[1:5] [1] "HALLMARK_HYPOXIA" "HALLMARK_CHOLESTEROL_HOMEOSTASIS" "HALLMARK_MITOTIC_SPINDLE" "HALLMARK_WNT_BETA_CATENIN_SIGNALING" "HALLMARK_TGF_BETA_SIGNALING"
up.CSEA.result<-CSEA2(targetScore=setNames(as.numeric(uniConSigResult$up.uniConSig), uniConSigResult$subjectID),compare.list=MyCompareList ,p.cut=0.05)

I hope this explanation is helpful.