Issue with mitochondrial gene enrichment?

[johanneswilbertz]

Thank you for providing this great toolbox! I have a question related to the enrichment of (mostly) mitochondrial genes.

When using the following code I get the expected result (plots below) when using GO_2018 terms, but not when using GO_2023. Importantly, I don't have that issue when using gene lists with less or no mitochondrial genes (MT-). Any idea what the issue could be here? Thanks!

# Gene sets
gene_sets_2018 = ['GO_Biological_Process_2018', 'GO_Molecular_Function_2018', 'GO_Cellular_Component_2018']
gene_sets_2023 = ['GO_Biological_Process_2023', 'GO_Molecular_Function_2023', 'GO_Cellular_Component_2023']
gene_sets = gene_sets_2023

# Gene list
DE_genes_list = ['MT-CO2', 'MT-CYB', 'MT-ND2', 'MT-ND3', 'MT-ND4', 'MT-ND1', 'MT-ATP6', 'MT-CO3', 'MT-RNR2', 'MT-RNR1', 'MT-ND4L', 'C12orf75', 'MTATP6P1']

# Perform GO enrichment analysis
enr = gp.enrichr(gene_list=DE_genes_list,
                 gene_sets=gene_sets,
                 organism='human', 
                 outdir=None)

# Convert results to a DataFrame
results = enr.results

Results using GO_2018

Results using GO_2023

For plotting I'm simply using this code in all cases:

# Function to plot top terms for each gene set with -log10(p-value)
def plot_top_terms(results, gene_set, top_n=20):
    df = results[results['Gene_set'] == gene_set].sort_values('Adjusted P-value').head(top_n)
    df['-log10(Adjusted P-value)'] = -np.log10(df['Adjusted P-value'])
    sns.set_context("talk")
    plt.rcParams["font.family"] = "Arial"
    plt.figure(figsize=(4, 6))
    sns.barplot(x='-log10(Adjusted P-value)', y='Term', data=df, palette='viridis')
    plt.title(f'Top {top_n} terms in {gene_set}')
    plt.xlabel('-log10(Adjusted P-value)')
    plt.ylabel('GO Term')
    plt.show()

# Plot top terms for each gene set
for gene_set in gene_sets:
    plot_top_terms(results, gene_set)

[zqfang]

I think the terms in GO_2023 database are changed.