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With the introduction of tissue microarrays (TMAs), another high-throughput method to investigate gene and protein expression is used in biological research at a regular basis, generating a wealth of data during production and use. Data management and data analysis are therefore a major concern to ensure on the one hand traceability and reproducibility of the experiment and on the other hand analysis in a timely and reliable fashion. Conventional spreadsheet based data organization is not feasible any more, robust and scalable applications have to be utilized, which allow data access and manipulation for researches from different laboratories in a secure way.

TAMEE (Tissue Array Management and Evaluation Environment) is a web-based database application for the management and analysis of data resulting from the production and experimental use of TMAs. In addition to production and experimental parameters images generated during the different stages of the TMA workflow are stored. Parameter values are based on structured classifications to ensure consistent database content which is the basis to yield biologically meaningful results in subsequent data analysis. Therefore existing public classifications are used and new controlled vocabularies have been defined in the context of the application. Tissue cores in the images of stained tissue sections are automatically located and extracted and can be automatically evaluated with a set of predefined analysis algorithms. Additional algorithms for the evaluation of tissue cores can be added to the application via a plug-in interface. Downstream analysis of the results is facilitated via a set of standard queries. More complex queries can be formulated with the help of a flexible query generator.

Thallinger GG, Baumgartner K, Pirklbauer M, Uray M, Pauritsch E, Mehes G, Buck CR, Zatloukal K, Trajanoski Z. TAMEE: data management and analysis for tissue microarrays. BMC Bioinformatics. 2007. 8:81. PMID: 17343750
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