Cnet plot showing non-significant genes within pathway

Question

[Mia]

Hi All,

I am trying to make cnet plots of differentially expressed genes between 2 tissue types, looking at specific pathways identified from enrichGO analysis. When I plot this a bunch of non-significantly regulated genes are appearing as uncolored dots and I am not sure how to stop this from happening so that my plots only include significantly regulated genes within the pathway of interest. I have attached an example of one of the cnet plots generated and am hoping someone knows how to fix this problem.

Here is the code I am using for the cnet:

>selected_pathways = "response to oxidative stress"

>cnetplot(eGO2, foldChange = geneListC57mnx_chow_iWAT_vs_eWAT, showCategory = selected_pathways, circular = FALSE, colorEdge = TRUE)

And the code for generating eGO2:

>eGO2 <- enrichGO(gene          = as.character(C57mnx_chow_sorted_gene_list$ensembl_gene_id),
                 OrgDb         = org.Mm.eg.db,
                 keyType = "ENSEMBL",
                 ont           = "ALL",
                 pAdjustMethod = "BH",
                 pvalueCutoff  = 0.01,
                 qvalueCutoff  = 0.05,
                 readable      = TRUE)

The file geneListC57mnx_chow_iWAT_vs_eWAT only includes genes that have a p.adjusted > 0.05 so I am confused as to why the plot is such a mess of insignificant genes. Any help would be much appreciated!

Answer 1

[Trivas]

I think the issue is that you're creating eGO2 with non-significant genes. Try subsetting C57mnx_chow_sorted_gene_list to your thresholds before sending it through enrichGO

[Trivas]

Saw you updated your post. You can have genes that are statistically significant (p-adj < 0.05) but still have a calculated l2FC < 1 (or whatever your threshold is). If you make a volcano plot, these points are pretty clear. I am suggesting you filter for both cut-offs before creating eGO2

[Mia]

Thanks so much. Both suggestions were very helpful!