WEGO2.0

WEGO2.0 visualizes and compares Gene Ontology (GO) annotation results across multiple datasets to quantify gene counts per GO ID and assess GO-term significance.

Key Features:

• Unlimited input files: Accepts an unrestricted number of GO annotation datasets for simultaneous analysis.
• Reference datasets: Includes reference GO datasets from nine model species for benchmarking comparative analyses.
• Chi-square multi-dataset statistical analysis: Performs Chi-square tests across multiple datasets to evaluate GO-term significance rather than pairwise comparisons.
• Output visualizations: Produces the traditional WEGO histogram and an additional graph that displays sorted P-values of GO terms to highlight significant differences among datasets.
• GO DAG-based aggregation: Utilizes the Directed Acyclic Graph (DAG) hierarchy of GO terms to calculate and visualize the number of genes associated with each GO ID across datasets.

Scientific Applications:

• Comparative GO analysis: Compare GO-term distributions and significance across multiple genomic, transcriptomic, or proteomic datasets.
• Functional annotation benchmarking: Benchmark novel organism GO annotations against reference datasets from model species.
• Gene expression functional profiling: Identify and visualize changes in GO-term representation across conditions or species to interpret gene expression patterns.

Methodology:

Processes GO annotation results as input; aggregates counts per GO ID using the GO Directed Acyclic Graph (DAG) hierarchy; performs Chi-square tests across multiple datasets; generates WEGO histograms and a graph of sorted P-values.