Hi,
I have a list of differentially expressed genes; I need a specific information for GOplot like below that comes from functional annotation of a list of genes
> head(GO[1:2,1:5])
Category ID Term
BP GO:0007507 heart development
BP GO:0001944 vasculature development
Genes
DLC1, NRP2 adj_pval
2.17e-06
1.04e-05
>
But I don't know how to get such a file. I tried DAVID, PANTHER, Enrichr but no one return such a file, for instance Enrichr does not return Category. Any of you know how to produce such a file by my gene list?
Thank you so much in advance
Can you specify what exactly you need (p-values, GO Term names...)? Is the code snipped supposed to illustrate what you already have?
Thank you I have a list of differentially expressed genes I need all of these 5 columns but each annotation tool just returns some of these columns. I'm wondering which returns such an output of functional annotation
Where is that code snippet from?
https://wencke.github.io/
Based on that link, I would be surprised if DAVID did not deliver the data.frame you need since it's explicitly mentioned that this is how the data.frame in the code snippet was generated. Anyway,
clusterProfiler
should be a good way to go, too as pointed out below.If you have list of HGNC Symbols to work with, you can split the data.frame above using
tidyr::separate_rows
and then usemerge
to get your results.I did not fid any tool returns this output directly