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| Code Block |
|---|
gene_fold_change_df = gene_expression_df %>% select(acronym,Section_Data_ID) %>% mutate(fold_change = gene_fold_change)
background_genes = gene_fold_change_df %>% arrange(desc(fold_change)) %>% pull(acronym)
target_genes = background_genes[1:7000]
gene_ontology_enrichment_df = GOrilla_run(
target.genes_target=target_genes,
background.genes_background=background_genes
) |
You can also find human diseases enriched in these mouse genes using the disease_ontology_enrichment_analysis function.
| Code Block |
|---|
disease_ontology_enrichment_df = disease_ontology_enrichment_analysis(
genes_target_genes=target_genes,
genes_background_genes=background_genes
)
disease_ontology_enrichment_df
# # A tibble: 11,703 x 6
# disease_id disease p q `Enrichment (N, B,... Genes
# <chr> <chr> <dbl> <dbl> <chr> <list>
# 1 C0596887 mathematical abili... 9.36e-8 0.000583 1.29 (12174,679,39... <chr [...
# 2 C0557874 Global development... 9.96e-8 0.000583 1.19 (12174,1434,3... <chr [...
# 3 C1305855 Body mass index 2.09e-7 0.000817 1.25 (12174,843,39... <chr [...
# 4 C0454644 Delayed speech and... 5.47e-7 0.00160 1.31 (12174,517,39... <chr [...
# 5 C4048268 Cortical visual im... 7.13e-7 0.00167 1.68 (12174,115,39... <chr [...
# 6 C3810365 Central visual imp... 1.29e-6 0.00252 1.72 (12174,98,397... <chr [...
# 7 C1858120 Generalized hypoto... 3.97e-6 0.00664 1.21 (12174,899,39... <chr [...
# 8 C0344482 Hypoplasia of corp... 4.97e-6 0.00708 1.35 (12174,335,39... <chr [...
# 9 C0232466 Feeding difficulti... 5.94e-6 0.00708 1.3 (12174,445,397... <chr [...
# 10 C0856975 Autistic behavior 6.05e-6 0.00708 1.44 (12174,222,39... <chr [...
# # ... with 11,693 more rows |
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