Storing, linking, and mining microarray databases using SRS.
BACKGROUND: SRS (Sequence Retrieval System) has proven to be a valuable platform for storing, linking, and querying biological databases. Due to the availability of a broad range of different scientific databases in SRS, it has become a useful platform to incorporate and mine microarray data to facilitate the analyses of biological questions and non-hypothesis driven quests. Here we report various solutions and tools for integrating and mining annotated expression data in SRS. RESULTS: We devised an Auto-Upload Tool by which microarray data can be automatically imported into SRS. The dataset can be linked to other databases and user access can be set. The linkage comprehensiveness of microarray platforms to other platforms and biological databases was examined in a network of scientific databases. The stored microarray data can also be made accessible to external programs for further processing. For example, we built an interface to a program called Venn Mapper, which collects its microarray data from SRS, processes the data by creating Venn diagrams, and saves the data for interpretation. CONCLUSION: SRS is a useful database system to store, link and query various scientific datasets, including microarray data. The user-friendly Auto-Upload Tool makes SRS accessible to biologists for linking and mining user-owned databases.
|Keywords||*Databases, Protein, *Software, Computational Biology/*methods, Data Collection, Gene Expression Profiling/methods, Information Storage and Retrieval/*methods, Oligonucleotide Array Sequence Analysis/*methods, User-Computer Interface|
|Persistent URL||dx.doi.org/10.1186/1471-2105-6-192, hdl.handle.net/1765/13873|
Veldhoven, A., de Lange, D., Smid, M., de Jager, V., Kors, J.A., & Jenster, G.W.. (2005). Storing, linking, and mining microarray databases using SRS.. B M C Bioinformatics, 6(192), 1–8. doi:10.1186/1471-2105-6-192