ADAM

ADAM performs Gene Set Enrichment Analysis (GSEA) by grouping genes from comparative samples across different species according to their functions and calculating significance p-values for gene diversity and activity.

Key Features:

• Cross-species analysis: Groups genes from comparative samples (control versus experiment) belonging to different species.
• Functional grouping: Classifies genes according to Gene Ontology and KEGG pathways as default functional categories.
• GFAG definition: Defines each group of genes as a GFAG (Group of Functionally Associated Genes).
• Significance calculation: Calculates p-values referring to gene diversity and activity to show functional group significance.

Scientific Applications:

• Comparative transcriptomics: Analyzes gene expression differences between control and experimental conditions across species.
• Functional enrichment analysis: Identifies significantly enriched Gene Ontology terms and KEGG pathways in comparative samples.
• Gene function annotation: Groups genes by shared functional associations to interpret biological meaning of expression changes.

Methodology:

ADAM calculates p-values referring to gene diversity and activity for groups of functionally associated genes.