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EMMA2 is a MAGE-compliant software platform for the evaluation of microarry experiment data sets resulting from genome-wide transcriptomics studies. EMMA2 allows to access the raw transcriptome data sets and provides automated and extensible analysis and visualization pipelines, including but not limited to the normalization of single and multiple microarrays and statistical tests for inferring differentially expressed genes. Also, co-regulated genes can be detected using integrated cluster analysis methods and gene expression can be mapped onto proteome data or pathways and vice versa. In addition to routine data analysis algorithms, the system can be integrated with other components containing additional data sources (e.g., genome annotation systems like GenDB). Detailed experimental setups and protocols as well as all raw data sets are provided to EMMA2 via ArrayLIMS, a separate microarray Laboratory Information Management System. ArrayLIMS allows to store the standardized data, i.e. the hybridization steps (e.g. RNA production), production of the hybridization targets, and the hybridization itself, as well as the raw images of the hybridized and the scanned slides with the corresponding data files.

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Funding: Service provision and maintenance funded by de.NBI.