SPOREBase - an internet accessible database consisting of diverse experimental data types for the study of lung cancer

Champion: Mark Burkart

Lung cancer research employs many different methods (e.g., expression microarray, array CGH, drug-sensitivity assays, etc.) that produce vast quantities of diverse types of data and experimental results. Naturally this data must be logically organized and efficiently stored to make the best use of it. However, this data is often multi-dimensional and highly complex in nature, and cannot be efficiently accessed when stored within a series of flat files or spreadsheets. Indeed, data stored in spreadsheets and similar formants must often be curated and distributed manually, and is more prone to contain errors. Relational databases, on the other hand, define how data are inter-related in advance, and complex relationships can be modeled within the structure of the database. Additionally, information in relational databases can be efficiently accessed, updated, distributed, and queried by automated script-driven methods.
SPOREBase is a web-accessible relational database of experimental data available to Lung SPORE researchers. SPOREBase currently houses information on a large number of cell lines, microarray probes, drug sensitivity experiments, and expression and aCGH experiments on multiple platforms. Batch downloads are available for array data and can be filtered using specific criteria (such as specific cell lines used). Downloads of array data can also be made using cell line lists filtered using drug sensitivity experiment criteria. Drug sensitivity data include dose-response measurements and summary IC-50 values and are filterable by such criteria as drug or cell line types used. Comprehensive annotation regarding all genes, cell lines, drugs, and experimental conditions are provided. SPOREBase will be expandable to include future experimental data types as needed and further capabilities can be provided on SPORE researchers' requests.

Recent Publications:

Burkart M.F., Wren J.D., Herschkowitz J.I., Perou C.M., Garner H.R. Clustering microarray-derived gene lists through implicit literature relationships. Bioinformatics. 2007 Aug 1;23(15):1995-2003. Epub 2007 May 30.
Zhang F., Sha J., Wood T.G., Galindo C.L., Garner H.R., Burkart M.F., Suarez G., Sierra J.C., Agar S.L., Peterson J.W., Chopra A.K. Alteration in the activation state of new inflammation-associated targets by phospholipase A2-activating protein (PLAA). Cell Signal. 2008 May;20(5):844-61. Epub 2008 Jan 17.