WTFgenes

WTFgenes performs gene set enrichment analysis to identify ontology-term associations in experimentally derived gene lists using statistical tests.

Key Features:

• Hypergeometric Distribution: Implements the hypergeometric test to assess the significance of gene enrichment within ontology terms.
• Model-Based Test (Collapsed Likelihood): Uses a collapsed likelihood framework for model-based gene set enrichment analysis.
• JavaScript Implementation: Provides an implementation in JavaScript that executes the analytical computations.
• C++11 Implementation: Provides a C++11 implementation with approximately twice the computation speed of the JavaScript version.

Scientific Applications:

• Gene list interpretation: Interprets gene lists derived from high-throughput experiments such as RNA sequencing and microarray analyses to identify significant ontology associations.
• Functional characterization: Elucidates biological processes, molecular functions, and cellular components associated with phenotypes or disease states.

Methodology:

Analyses are based on the hypergeometric test and a model-based analysis employing a collapsed likelihood approach.