CompGO

CompGO performs comparative Gene Ontology (GO) and pathway enrichment analysis as an R/Bioconductor package to identify differentially enriched GO terms and pathways between DNA-binding or genomics experiments.

Key Features:

• Differential Enrichment Analysis: Computes z-scores derived from log odds ratios to identify Differentially Enriched Gene Ontologies (DiEGOs) and pathways between experiments.
• Statistical Framework: Adapts a log odds ratio z-score approach used in epidemiological studies to provide statistical justification for comparative GO analyses.
• Visualization: Produces visual representations of differences at both GO term and pathway levels.
• Data Integration: Accepts inputs such as .BED files containing genomic coordinates and gene lists for incorporation into analysis workflows.

Scientific Applications:

• Systems Biology and Genomics: Detection and interpretation of differential GO enrichment in systems biology and genomics studies.
• Comparative DNA-binding Analysis: Comparison of GO enrichment between DNA-binding experiments to reveal subtle differences in regulatory activity.
• Public Experimental Data Analysis: Application to public datasets, including studies involving the cardiac transcription factor NKX2-5.

Methodology:

Calculation of z-scores derived from log odds ratios to assess differential enrichment, with comparison against traditional overlap methods and integration of experimental data.