Hi.

I work with Prunus persica. Goseq doesn't support it so I perform the GO Analysis 'by hand' like this:

>de_data=read.table("gene_exp.diff", header=T)
>diff_express=de_data$dea
>names(diff_express)=de_data$gene
>length=de_data$length
>cat_map=read.csv("godata.txt", header=FALSE, sep="\t")
>pwf=nullp(diff_express, bias.data=length, plot.fit=TRUE)
>GO.wall=goseq(pwf, gene2cat=cat_map)

Then I save the GO.wall output, who looks like the one reported on goseq User's guide.

What I need is a list of all my genes paired with the gene ontology term and with the 'term' and 'ontology'. Goseq just report the totals (ej: 800 genes are 'BP' and 'single-organism cellular process').

In other words I want to answer the question: which prunus persica genes are part of the term 'single-organism cellular process' under the ontology 'Biological Process'?.

Thanks in advance.

All information about which genes are in each go term is in the data.frame 'cat_map' that you created yourself. To look at any individual GO term, you can just subset your own data.frame.

Similar questions have been asked before. You might find these threads useful.

Can I know the number of genes in enriched GO category using GOseq

goseq analysis - extracting list of my genes which are DE in the enriched GO category

How to get list of genes that are DE from the goseq analysis results

Cheers,

Nadia.