Transparent Gene Set Enrichment Analysis

Prerequisites

• Have a text file with a set of newline-separated background genes in /data/backgrounds.
• Place gene set library files in the Gene Matrix Transposed format in /data/libraries.
• alias.json files provides human-readable names for gene set libraries and background gene sets.

Run the Application

• To run locally, use streamlit run code/streamlit.app
• To run in Docker use docker build -t cc_enrichment:latest . and docker run -p 8501:8501 co_enrichment:latest

Overview of Application Components

Key Features

Gene Set Submission

Users have the flexibility to input their gene set in two ways:

• Direct Input: Paste a newline-separated list of gene names and assign a name to the gene set.
• File Selection: Choose an existing gene list from the local data folder.

Gene Set Validation

The app performs crucial validation steps to ensure the accuracy of the analysis:

• Duplicate Check: It checks for any duplicate gene names within the input gene set.
• Background Check: It validates the input gene set against a predefined background gene set, which helps in identifying any genes that might not be present in the background set.

Results Display and Interaction

• Interactive Chart: The results for each gene set library are displayed in an interactive chart, allowing users to engage with the data dynamically.
• Interactive Bar Graph: An interactive bar graph provides a visual representation of the results for each gene set library.

Data Export Options

• Individual Library Export: Users can save the results for each gene set library in TSV and JSON formats.
• Consolidated Export: There is an option to save results for all libraries in a single TSV file.

Results Management

All results, along with the complementary metadata, are stored in the results folder and are assigned unique filenames.

Advanced Features

Customization of Results Display

Users can customize the number of results to display in both the chart and the bar graph in the Streamlit app.

P-value Calculation Methods

The app offers various statistical methods to calculate p-values:

• Fisher's Exact Test.
• Hypergeometric Test.
• Chi-Squared Test.

Custom Reference Data Upload

Background Gene Set Upload: Users can upload their background gene sets as .txt files containing newline-separated gene names. Gene Set Libraries Upload: The app allows for the upload of gene set libraries in the .gmt file format, enabling the use of custom gene sets in the analysis.