GOTrapper

GOTrapper enables exploration and analysis of Gene Ontology (GO) term associations and hierarchical navigation for gene sets to support functional interpretation.

Key Features:

• Hierarchical Navigation: Supports manual traversal of the GO hierarchy both upwards and downwards to explore biological functions at different specificity levels.
• Threshold-based Control: Uses an assigned threshold parameter to guide the depth of traversal within the ontology hierarchy.
• Input Configurations ("Within" / "Between"): Provides a "Within" mode to identify associated GO terms within a single gene list and a "Between" mode to compare GO associations between two distinct gene lists.
• Evidence Code Filtering: Filters retrieved GO terms by specified evidence codes to restrict results to selected experimental evidence types.
• Shared GO Term Retrieval: Identifies GO terms shared across user-provided gene sets to highlight common functional annotations.
• Implementation: Implemented as a Java application.

Scientific Applications:

• Hypothesis Generation: Identify shared GO terms among input genes to generate hypotheses about gene function and biological processes.
• Differential Gene Expression Analysis: Link GO terms to differentially expressed genes to aid interpretation of expression changes.
• Comparative Genomics: Compare GO term associations between gene lists to assess functional similarities or differences between conditions or groups.

Methodology:

GOTrapper retrieves shared GO terms from user-defined gene lists (including Homo sapiens), leverages the structured GO hierarchy for upward and downward traversal, and applies user-set thresholds and evidence code filters to refine returned GO terms.