Basic Examples¶

This page provides basic examples of using GeneInsight for gene set analysis.

Example 1: Human Gene Set Analysis¶

This example demonstrates the basic workflow for analyzing a human gene set.

Input Preparation¶

Save your gene list in a text file with one gene per line:

genes_of_interest.txt¶

BRCA1
BRCA2
TP53
ATM
CHEK2
PALB2
RAD51
BARD1

Similarly, prepare a background gene list:

background_genes.txt¶

# This file contains a larger set of genes for statistical comparison
# Format: one gene per line
BRCA1
BRCA2
TP53
ATM
CHEK2
PALB2
RAD51
BARD1
# ...many more genes...

Running the Analysis¶

Execute GeneInsight with default parameters:

geneinsight genes_of_interest.txt background_genes.txt -o ./dna_repair_analysis

This will:

Retrieve functional annotations from the STRING database
Perform topic modeling to identify biological themes
Apply statistical validation through hypergeometric testing
Generate an interactive HTML report

Exploring the Results¶

Navigate to the output directory and open the HTML report:

cd dna_repair_analysis
# Open unzip sphinx_build.zip and open index.html in your browser