Getting this specific information from gene- annotation enrichment analysis

Question

[zizigolu]

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

[Friederike]

Can you specify what exactly you need (p-values, GO Term names...)? Is the code snipped supposed to illustrate what you already have?

[zizigolu]

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

[Friederike]

Where is that code snippet from?

[zizigolu]

https://wencke.github.io/

[Friederike]

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.

[Ram]

If you have list of HGNC Symbols to work with, you can split the data.frame above using tidyr::separate_rows and then use merge to get your results.

[zizigolu]

I did not fid any tool returns this output directly

Answer 1

[H.Hasani]

Hello F,

part of the output you are showing is a standard result of any enrich function from package clusterProfiler in R.
For instance, in the example above, the Category column = BP, this mean the user used function enrichGO with ont = BP, so ego = enrichGO(geneList, ont = "BP", ...). the object ego typically will have the following info in its results part ID, Description, GeneRatio, BgRatio, pvalue, p.adjust, qvalue, geneID, Count you can of course filter the columns you want, in this case: ID, Description, p.adjust, geneID, then rename the columns and add column Category = BP at the end.

hth

Answer 2

[annie.wong]

Must be really obvious to people already familiar with these programs but not to newbies like myself. You can get the input data from DAVID.

You have to Upload your DE genes into DAVID website on the left hand of the home page. Select identifier, then Analyse. Once analysed, you have to use the 'Functional Annotation Chart'. Save this doc link as txt. Open this doc in Excel, deliminating by tab and the genes used in each GO term is listed in one of the columns:

Category, Term, Count, %, PValue, Genes, List, Total, Pop Hits, Pop Total, Fold Enrichment, Bonferroni, Benjamini, FDR.