How to annotate gene list using enrichr?

Question

[nattzy94]

I am analysing a published rnaseq read counts table that is upper quartile normalised. I have correlated a transcript of interest (transcript A) against all other transcripts and obtained a 2 column table with transcript/gene names in the first column and Pearson correlation (ranging from -1 to 1) in the second column. I want to annotate the gene list so that I can get the gene function in a 3rd column. I've passed the list of genes into enrichr but the list of gene functions that it returns is not the same length as the list of genes that I passed in. Any ideas on how else I can do this?

[b.bearmi]

not all the genes have annotated functions? Can you give an example of what enrichr has skipped?

[nattzy94]

It's skipped about 3000 genes. I passed ~8000 genes into queryMany using the GoBiologicalProcess db. The resulting GO_Biological_Process_2018$Genes only has 5000 entries.

Should I include the correlation values when I input the data into queryMany?

Answer 1

[Kevin Blighe]

There may be an issue with ID matching, or it may be that it simply could not enrich those 3000 'missing' genes. No need to input the correlation values, as it won't use them and may throw a syntax error.

Another thing to check is thresholds used for enrichment:

• minimum genes per enrichment term
• p-value

Kevin