Which genes are in each GO termn

[Jomagrax]

I have performed GO enrichment and obtained the barplot, I was wondering if it is possible to obtain the list of the genes present in each Go term

Thanks in advance

[tiagochst]

You can access the objects with the genes as following:

TCGAbiolinks:::DAVID_MF_matrix %>% as_tibble() TCGAbiolinks:::DAVID_CC_matrix %>% as_tibble() TCGAbiolinks:::listEA_pathways %>% as.tibble() TCGAbiolinks:::DAVID_BP_matrix %>% as_tibble()

[image: Screenshot 2023-07-05 at 12.07.03 PM.png]

On Wed, Jul 5, 2023 at 10:51 AM Jomagrax @.***> wrote:

I have performed GO enrichment and obtained the barplot, I was wondering if it is possible to obtain the list of the genes present in each Go term

Thanks in advance

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[Jomagrax]

Thanks Tiago,

With you answer I was able to produce what I needed

Here you have an example for the "Biological Process" GO term Genelist is produced as in here

# Download genes in each GO class
TCGAbiolinks:::DAVID_MF_matrix %>% as_tibble()
TCGAbiolinks:::DAVID_CC_matrix %>% as_tibble()
TCGAbiolinks:::listEA_pathways %>% as_tibble()
bp_DB <- TCGAbiolinks:::DAVID_BP_matrix %>% as_tibble()

## Go terms present in the barplot have to  be introduced manually
GO <- c("nuclear division","mitosis")

bp_DEG <- bp_DB  %>%
   mutate(DavidBP = sub("^.{11}", "", DavidBP))     %>%  
   filter(DavidBP %in% GO ) %>%               # Application of separate_rows() function
   separate_rows(Molecules, sep=",") %>%
   mutate(Molecules = sub("^.{1}", "", Molecules)) %>% 
   filter(Molecules %in% Genelist) %>%   
   as.data.frame()