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. 2009 Feb 6:10:50.
doi: 10.1186/1471-2105-10-50.

EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data

Michael Dondrup  1 , Stefan P Albaum, Thasso Griebel, Kolja Henckel, Sebastian Jünemann, Tim Kahlke, Christiane K Kleindt, Helge Küster, Burkhard Linke, Dominik Mertens, Virginie Mittard-Runte, Heiko Neuweger, Kai J Runte, Andreas Tauch, Felix Tille, Alfred Pühler, Alexander Goesmann
Affiliations

EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data

Michael Dondrup et al. BMC Bioinformatics. .

Abstract

Background: Understanding transcriptional regulation by genome-wide microarray studies can contribute to unravel complex relationships between genes. Attempts to standardize the annotation of microarray data include the Minimum Information About a Microarray Experiment (MIAME) recommendations, the MAGE-ML format for data interchange, and the use of controlled vocabularies or ontologies. The existing software systems for microarray data analysis implement the mentioned standards only partially and are often hard to use and extend. Integration of genomic annotation data and other sources of external knowledge using open standards is therefore a key requirement for future integrated analysis systems.

Results: The EMMA 2 software has been designed to resolve shortcomings with respect to full MAGE-ML and ontology support and makes use of modern data integration techniques. We present a software system that features comprehensive data analysis functions for spotted arrays, and for the most common synthesized oligo arrays such as Agilent, Affymetrix and NimbleGen. The system is based on the full MAGE object model. Analysis functionality is based on R and Bioconductor packages and can make use of a compute cluster for distributed services.

Conclusion: Our model-driven approach for automatically implementing a full MAGE object model provides high flexibility and compatibility. Data integration via SOAP-based web-services is advantageous in a distributed client-server environment as the collaborative analysis of microarray data is gaining more and more relevance in international research consortia. The adequacy of the EMMA 2 software design and implementation has been proven by its application in many distributed functional genomics projects. Its scalability makes the current architecture suited for extensions towards future transcriptomics methods based on high-throughput sequencing approaches which have much higher computational requirements than microarrays.

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Figures

Figure 1
Figure 1
Architecture of the EMMA 2 software. EMMA 2 is built by combining a three-tier architecture in combination with a model-view-controller (MVC) design pattern. In contrast to the standard three-tier approach, the back-end-layer (bottom) contains an object-relational mapping layer (O2DBI). The business-layer contains the application logic and provides data integration features. The presentation layer provides two modes of presenting data.
Figure 2
Figure 2
The web-interface of the EMMA 2 software. EMMA 2 provides a highly user friendly web-interface with integrated help and documentation. The top image depicts the entry page to each project. The image below shows the overview of an experiment. The outcomes of data-analyses are depicted as icons at the bottom of the page.
Figure 3
Figure 3
Management of experimental factors. Experimental factors and their values are integrated in the web-interface. The screenshots show how measurement units can be defined using the MGED ontology (top). Array data can be assigned to factor values by the use of a drag-and-drop mechanism to build the experiment design matrix.
Figure 4
Figure 4
The integrated applet for viewing clusters. An integrated solution for cluster analysis is provided. The tree-viewer applet allows intuitive inspection of trees and heatmaps. The tree can be cut at arbitrary heights and the resulting clusters can be further inspected (bottom). Vector and pixel graphics of the tree and the clusters can be exported.
See this image and copyright information in PMC

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