JProGO

JProGO performs functional interpretation of prokaryotic microarray gene expression data by applying Gene Ontology (GO) annotations to identify altered gene groups and biological processes.

Key Features:

• Statistical Analysis Methods: Implements Fisher's Exact Test (threshold-dependent), Kolmogorov–Smirnov and Student's t-test (threshold-independent), and Wilcoxon's rank-based unpaired test for GO-based microarray analysis.
• Multiple Testing Correction: Applies correction procedures for multiple comparisons to control false positives in enrichment analyses.
• Alternative Gene Name Recognition: Recognizes alternative gene names to improve mapping between microarray probes and GO annotations.
• Visualization of Results: Produces GO subgraphs highlighting significant nodes and detailed result tables for interpreted gene sets.
• Species Coverage: Supports analysis of microarray data from over 20 different prokaryotic species, including key model organisms.

Scientific Applications:

• GO-based Functional Interpretation: Interprets differential gene expression in prokaryotic microarray datasets through GO-term enrichment and ranking.
• Condition-specific Process Identification: Identifies biological processes and gene groups affected under different experimental conditions.
• Microbial Genomics and Applied Studies: Supports basic microbial research and applied investigations in biotechnology and medicine that rely on GO-informed expression analysis.

Methodology:

Integrates GO functional annotation with statistical tests (Fisher's Exact Test, Kolmogorov–Smirnov, Student's t-test, Wilcoxon's rank-based unpaired test) and applies multiple-testing correction to identify significant GO terms.