enrichGO function produces NULL object

Question

[rykers]

Hi all,

I am doing a enrichment analysis of a list of genes gathered from previous WGCNA analysis. When I run the enrichGO function on my gene list however, nothing happens. There is no verbose output and the result is a NULL valued object.

I have researched a bit about how to correct this and removed any pvalue cutoffs that may prevent ontologies from being discovered. These are all the libraries and variables as well as what is in my original gene list object. I am using R version 4.4.0

library(clusterProfiler)
library(enrichplot)
library(ggplot2)
library(DOSE)

organism = "org.At.tair.db"
head(gene_list)

---

  > head(gene_list)
                  x
AT5G14210 0.9857885
AT5G66950 0.9841047
AT1G05805 0.9823505
AT2G38970 0.9808063
AT5G56530 0.9803802
AT2G32560 0.9803239

Below is the function call and all arguments used as the resulting output. The output is the same regardless of if I specify a pvalue cut off or not.

ego <- enrichGO(gene=gene_list,
                            OrgDb= organism,
                            ont= "ALL",
                            keyType = "TAIR",
                            pAdjustMethod = "none",
                            pvalueCutoff = 1,
                            qvalueCutoff = 1,
                            minGSSize =1)

 ego
 head(summary(ego))

---

    > ego
    NULL

    > head(summary(ego))
    Length  Class   Mode 
         0   NULL   NULL

Any and all help in explaining why the function is not calling appropriately would be greatly appreciated. I am certain that the input data is in the correct format and believe I am missing something with the function itself. Thank you!

Answer 1

[bk11]

You need to supply gene list only and not the values present in column x.

genes <- c("AT5G14210","AT5G66950","AT1G05805","AT2G38970","AT5G56530","AT2G32560")
# or do this, genes <- c(rownames(gene_list))

ego <- enrichGO(gene=genes,
                            OrgDb= organism,
                            ont= "ALL",
                            keyType = "TAIR",
                            pAdjustMethod = "none",
                            pvalueCutoff = 1,
                            qvalueCutoff = 1,
                            minGSSize =1)

head(summary(ego))
           ONTOLOGY         ID                                             Description GeneRatio  BgRatio       pvalue     p.adjust qvalue    geneID Count
GO:1901379       BP GO:1901379     regulation of potassium ion transmembrane transport       1/1  3/21061 0.0001424434 0.0001424434     NA AT1G05805     1
GO:1903286       BP GO:1903286                      regulation of potassium ion import       1/1  3/21061 0.0001424434 0.0001424434     NA AT1G05805     1
GO:0043266       BP GO:0043266                   regulation of potassium ion transport       1/1  8/21061 0.0003798490 0.0003798490     NA AT1G05805     1
GO:1904062       BP GO:1904062 regulation of monoatomic cation transmembrane transport       1/1  9/21061 0.0004273301 0.0004273301     NA AT1G05805     1
GO:1990573       BP GO:1990573             potassium ion import across plasma membrane       1/1 11/21061 0.0005222924 0.0005222924     NA AT1G05805     1
GO:0034765       BP GO:0034765    regulation of monoatomic ion transmembrane transport       1/1 13/21061 0.0006172546 0.0006172546     NA AT1G05805     1