GO_analysis

GO_analysis is a command-line Java tool for performing Gene Ontology (GO) enrichment analysis and processing gene-to-GO term mappings. It supports statistical evaluation (hypergeometric, Fisher's exact, and Kolmogorov-Smirnov tests) and multiple testing correction, helping users identify enriched GO terms among gene sets.

Features

• Parses GO term relationships from .obo files.
• Processes gene-to-GO mappings in various formats.
• Supports enrichment analysis using hypergeometric, Fisher's exact, and KS tests.
• Applies Benjamini-Hochberg correction for multiple testing.
• Handles custom gene lists and mapping types.
• Outputs results and enrichment statistics to files.

Usage

1. Build the project (ensure you have Java and any required dependencies):

   javac -d bin src/*.java

2. Run the program with required options:

   java -cp bin Main \
     -obo path/to/go.obo \
     -root NAMESPACE \
     -mapping path/to/mapping_file \
     -mappingtype [go|ens] \
     -enrich path/to/enrichment_file \
     -o output_path \
     -minsize MIN_GO_SIZE \
     -maxsize MAX_GO_SIZE

   Optional:
   Add -overlapout path/to/overlap_output to include overlap statistics.

Arguments

• -obo : Path to GO .obo ontology file.
• -root : GO namespace/root term (e.g., BP/CC/MF).
• -mapping : File with gene-to-GO mappings.
• -mappingtype : Mapping type (go or ens).
• -enrich : File with input gene list (for enrichment).
• -o : Output file path for results.
• -minsize : Minimum GO term size to consider.
• -maxsize : Maximum GO term size to consider.
• -overlapout : (Optional) Output file for overlap results.

To display help:

java -cp bin Main

Input File Formats

• OBO file: Standard GO ontology format.
• Mapping file: Tab-separated gene-to-GO relationships.
• Enrichment file: List of genes (optionally with fold change and significance).

Output

The tool generates enrichment results including GO terms, associated genes, p-values, FDR, and optionally overlap statistics.