Why output enrichment analysis Reactome with the same gene list?
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Entering edit mode
11 months ago
camillab. ▴ 40

Hi,

I have tried to perform enrichment analysis on reactome with a list of 481 genes. I have tried using reactomePA (R package), reactome website analysis tool, and enrichR (which has reactome2016 database) and I got different results:

ReactomePA: 843 terms

Reactome analysis tool: 1277 terms

Reactome 2016 enrichR: 788 terms

Since enrichR is older compare to the others, I am not surprised to have fewer terms but I dont understand why comparison reactomePA and reactome analysis tool I got so different results. is it possible that I wrote a wrong script for reactomePA?

My dataset looks like:

# A tibble: 6 x 2
Entrezgene_ID log2fc
<chr>          <dbl>
1 14             -1.02
2 80755          -1.45
3 60496          -1.17
4 6059           -1.48
5 10061          -1.35
6 10006          -1.51


and my code for reactomePA is:

#load packages
library(org.Hs.eg.db) #human genome
library(DOSE)
library(ReactomePA) # to perform enrichment analysis

#organise the datasets
genes <- d[[2]] #numeric vector #selected log2fc
names(genes) <- d[[1]] #named vector
geneLIST <- sort(genes, decreasing = TRUE) #decreasing order

de <- names(geneLIST)
x@result # 843 terms


Did I have done something wrong?

Camilla

reactome enrichment RNA-Seq R enrichR • 312 views
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Entering edit mode

The devil's probably in the detail of the parameters chosen by both enrichPathway` and the REACTOME website. You'd have to dig into the documentation of both tools to, for example, understand (a) how the enrichment's significance (p-value) is calculated, (b) whether there are any additional corrections/calculations and (c) which thresholds are used to determine the final output.