ADGO

ADGO performs composite Gene Ontology-based gene set enrichment analysis of microarray data to identify intersected gene sets and interpret differential expression.

Key Features:

• Composite Annotations: Integrates multiple Gene Ontology (GO) categories to generate intersected gene sets that reveal composite biological themes beyond single-category annotations.
• Gene Set Analysis Methods: Supports various gene set analysis methods for microarray data inputs to perform enrichment analyses on gene lists.
• Redundancy Screening (ADGO 2.0): Screens and filters redundant composite annotations during generation and prioritization of results.
• Set Operations: Performs union, subtraction, and intersection operations on gene sets for flexible set-based analyses.
• Custom Gene Set Uploads: Accepts uploaded custom gene sets, including predicted miRNA targets, for generation and analysis of new composite sets.
• Platform and Species Support: Supports analysis of Affymetrix and dual-channel array data for human, mouse, rat, and yeast.
• Scoring of Expression Changes: Scores expression changes across single and intersected sets to identify significant composite terms.

Scientific Applications:

• Differential Gene Expression Analysis: Detects enriched single and composite GO terms from microarray-derived gene lists to interpret differential expression.
• T-cell Differentiation Studies: Applied to analyses of gene expression changes related to T-cell differentiation.
• HIV-1 Immune Response Studies: Applied to analyses of gene expression changes associated with HIV-1 immune response.
• Disease Mechanism Discovery: Identifies significant composite terms that provide insights into disease mechanisms and biological processes.

Methodology:

Intersect annotated gene sets from different GO categories and score expression changes across single and intersected sets; generate and prioritize composite annotations and screen for redundant composites (ADGO 2.0); perform set operations (union, subtraction, intersection) on gene sets.