Dear all,

What is the most recent and reliable gene ontology tool in Python? I am currently using Enrichr in but it seems that some of the terms always appear as significant when I use my DE candidates (with the background set of Biological Processes 2021) and also when I use some random genes.

I feel that the problem could be because of the Enrichr but not completely sure. Here is my code:

import pandas as pd
import gseapy as gp
from gseapy.plot import barplot, dotplot
import matplotlib.pyplot as plt

#Available databases : ‘Human’, ‘Mouse’, ‘Yeast’, ‘Fly’, ‘Fish’, ‘Worm’
gene_set_names = gp.get_library_name(database='Human')
#print(gene_set_names)

file=pd.read_csv("my_target_genes.csv",header=None)
#print(file)

#to make a list from target genes
glist = file.squeeze().str.strip().tolist()
#print(glist)


enr = gp.enrichr(gene_list=glist,
                     organism='Human',
                     gene_sets='GO_Biological_Process_2021',
                     description='pathway')

dotplot(enr.res2d,cmap='viridis_r', ofname='GO_output',column='Adjusted P-value',cutoff=0.05, top_term=20,)

Thank you.