title: TAMEE: data management and analysis for tissue microarrays.
abstract: BACKGROUND
  With the introduction of tissue microarrays (TMAs) researchers can investigate gene and protein expression in tissues on a high-throughput scale. TMAs generate a wealth of data calling for extended, high level data management. Enhanced data analysis and systematic data management are required for traceability and reproducibility of experiments and provision of results in a timely and reliable fashion. Robust and scalable applications have to be utilized, which allow secure data access, manipulation and evaluation for researchers from different laboratories.
  
  
  RESULTS
  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 application of TMAs. It facilitates storage of production and experimental parameters, of images generated throughout the TMA workflow, and of results from core evaluation. Database content consistency is achieved using structured classifications of parameters. This allows the extraction of high quality results for subsequent biologically-relevant data analyses. Tissue cores in the images of stained tissue sections are automatically located and extracted and can be evaluated using a set of predefined analysis algorithms. Additional evaluation algorithms can be easily integrated into the application via a plug-in interface. Downstream analysis of results is facilitated via a flexible query generator.
  
  
  CONCLUSIONS
  We have developed an integrated system tailored to the specific needs of research projects using high density TMAs. It covers the complete workflow of TMA production, experimental use and subsequent analysis. The system is freely available for academic and non-profit institutions from http://genome.tugraz.at/Software/TAMEE.
authors.affiliation: Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria. Gerhard.Thallinger@tugraz.at <Gerhard.Thallinger@tugraz.at>
authors.forename: Gerhard G
authors.initials: GG
authors.lastname: Thallinger
authors.forename: Kerstin
authors.initials: K
authors.lastname: Baumgartner
authors.forename: Martin
authors.initials: M
authors.lastname: Pirklbauer
authors.forename: Martina
authors.initials: M
authors.lastname: Uray
authors.forename: Elke
authors.initials: E
authors.lastname: Pauritsch
authors.forename: Gabor
authors.initials: G
authors.lastname: Mehes
authors.forename: Charles R
authors.initials: CR
authors.lastname: Buck
authors.forename: Kurt
authors.initials: K
authors.lastname: Zatloukal
authors.forename: Zlatko
authors.initials: Z
authors.lastname: Trajanoski
mesh_terms: D000465:Algorithms; D003628:Database Management Systems; D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods*; D016247:Information Storage and Retrieval / Q000379:methods*; D020407:Internet; D012984:Software; D046888:Tissue Array Analysis / Q000379:methods*; D014584:User-Computer Interface