Enrichment Analysis significance cutoff

[Semple-bio]

Good day. There are 2 adj. p-value cutoff used in the 'Enrichment Analysis' part, where the secondary is redundant as the first one is more stringent.

First cutoff, at 0.001 level:

#data for plotting
PathwaysSelect <- sig_pathways_df %>%
    dplyr::select(pathway, `p-value`, `Adjusted p-value`) %>%
    dplyr::filter(`Adjusted p-value` <= 0.001) %>%
    dplyr::rename(pvalue = `p-value`, AdjPvalu = `Adjusted p-value`) %>% 
    dplyr::mutate(pathway = as.factor(pathway))

Second cutoff, with no effect:

ggdata = PathwaysSelect %>% 
    dplyr::filter(AdjPvalu <= 0.05) %>% 
    dplyr::group_by(source) %>% 
    dplyr::arrange(AdjPvalu) %>%
    dplyr::slice(1:5)