EMMA2

EMMA2 provides comprehensive analysis and management of genome-wide transcriptomics microarray data and enforces MIAME-compliant annotation through MAGE-ML and ontology support.

Key Features:

• Supported platforms: Supports spotted arrays and synthesized oligo arrays including Agilent, Affymetrix, and NimbleGen.
• MAGE-ML and ontology support: Implements the MAGE-ML format and ontology support to standardize microarray data annotation consistent with MIAME.
• Full MAGE object model: Implements a full MAGE object model through a model-driven approach for data representation and flexibility.
• Genomic annotation integration: Integrates genomic annotation and external knowledge sources using open standards.
• Statistical analysis: Performs statistical testing for differential expression using R and Bioconductor packages.
• Distributed computation: Can utilize compute clusters to provide distributed analysis services.
• Web-service data integration: Supports SOAP-based web services for distributed data integration in client-server environments.
• Scalability: Architecture is designed to scale for extensions toward high-throughput sequencing technologies requiring greater computational resources.

Scientific Applications:

• Differential expression analysis: Identification of differentially expressed genes from genome-wide microarray experiments using R and Bioconductor statistics.
• Transcriptional regulation and gene relationships: Analysis of transcriptional regulation to unravel complex gene relationships from microarray data.
• Functional genomics studies: Integration of microarray results with genomic annotation and external knowledge for functional genomics projects.
• Distributed collaborative analysis: Enables collaborative analysis across distributed research consortia via SOAP-based data integration and distributed services.

Methodology:

Implements MAGE-ML with ontology support and a model-driven full MAGE object model; performs analysis using R and Bioconductor packages; supports compute cluster-based distributed services and SOAP-based web-service data integration; integrates genomic annotation via open standards.