AMEN

AMEN integrates and analyzes genomic and proteomic datasets to perform genome annotation, chromosomal mapping, protein–protein interaction analysis, expression profiling, and proteomics data management.

Key Features:

• Data upload and pre-processing: Accepts and pre-processes microarray expression profiling data for downstream analysis.
• Co-expression analysis: Detects groups of significantly co-expressed genes to identify gene clusters with shared regulation or function.
• Functional annotation enrichment: Searches for enrichment of functional annotations within identified gene groups to aid biological interpretation and pathway analysis.
• Genome annotation: Provides functionality for genome annotation across analyzed datasets.
• Chromosomal mapping: Supports mapping of genes and features to chromosomes.
• Protein–protein interaction analysis: Integrates and visualizes protein–protein interaction networks.
• Expression profiling: Performs analysis and visualization of expression profiles.
• Proteomics data management: Manages proteomics datasets for integration with genomic and expression data.

Scientific Applications:

• Expression profiling interpretation: Applied to interpret microarray expression profiling data across organisms including budding yeast, rodents, and humans.
• Molecular systems biology: Used to analyze high-throughput genomic datasets for exploration of complex biological networks and interactions.

Methodology:

Performs upload and pre-processing of microarray expression data, detection of significantly co-expressed gene groups, functional annotation enrichment analysis, and visualization of protein–protein interaction networks, expression profiles, and cellular co-localization patterns.