GCC: a database system for immune cells transcriptomes

Andrea Splendiani1, C.Vizzardelli,N.Pavelka,M.Pelizzola,M.Capozzoli,O.Beretta,F.Granucci,P.Ricciardi-Castagnoli
1andrea.splendiani@unimib.it, Univ. Milano Bicocca

GCC is a database collecting information on immune cells responses to different microorganims. Transcriptional profiles of dendritic cells (DCs) in response to different microorganisms have been analyzed using microarrays and annotated data is stored in a database, allowing for unbiased exploration of the immune response. A web-driven database system based on opensource technologies underlies this project. It was designed to achieve usability, flexibility and to allow for MIAME compliant experimental annotation. It is targeted specifically at the Affymetrix platform, and it handles coherently specific files and data types, without the overhead required to handle different platforms. It offers a rich support for experimental annotation. It supports an experimental structure that can be customized for specific research areas, also allowing for the use and development of controlled vocaboularies and ontologies. It provides a flexible access policy allowing for several level of visibility and manteinance. Experiment annotation in particular is checked for consistency and to avoid accidental errors and data corruption. The system exports data in several formats, allowing for quick integration with data analysis tools. Future extension planned are export in MAGE-ML format and integration of MAGE-ML Affymetrix chip description files.