ACCG

The Anderson Cancer Center Genomics Database

Both microarrays and SAGE generate tremendous amounts of data. The response at The M. D. Anderson Cancer Center has been to develop a database to store both kinds of data, in a way that will allow us to connect the gene expression values to information about sample sources.

An overview of the microarray portion of the database breaks the design into the following sections:

• Project management tools, which provide security by controlling which users and groups can access what data;
• Sample source information, which provides the connections to other databases containing details about the RNA source;
• Information about the physical microarrays used, which is separate from the logical
• Design of the microarray, which means both the geometry of the spots as well as details about the biological material placed at each spot of the array;
• Experiment information about the conditions under which the RNA sample was hybridized to the cDNA microarray;
• Images of the hybridized arrays;
• Analysis of the images, which must at least contain the quantifications of gene expression levels at each spot.

A more complete picture of the tables in the database design is available. (One should note that this picture is a historical document; the actual design has changed in minor ways since the picture was prepared.)

The original design of the database was directed at the storage of microarray data, since that technology was expected to come on line first at M. D. Anderson. It soon became clear, however, that significatn portions of the design could be re-used to store SAGE data. In particular, the security mechanisms built into the project management tools and the sample source information work the same way in both cases. The only change needed was to add additional tables to hold the SAGE data.

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