TRANSCRIPTOME 2002: From Functional Genomics to Systems
PGA-CPR (Chip Profiling Resource): A Web Queried Database of Affymetrix Profiles with Cross-Profile Analysis Tools
Josephine Chen, Dietrich Stephan, and Eric Hoffman, Research Center for Genetic Medicine, Children’s National Medical Center, Washington, DC
The centralized public resource of genomic DNA sequence, and SNPs that have facilitated research world-wide, while also minimizing redundancy in data generation by different laboratories. Development of a similar centralized database of mRNA information (expression profiles) has been hampered by issues such as standardization of data generation, reporting, and storage. Here, we present standard operating procedures, quality control measures, and uniform data reporting enabling a centralized Oracle database of expression profiles (1,300 to date). We have built an SQL web interface to this data warehouse, allowing on-line queries of all profiles by any number of experimental variables (tissue, species, chip type, etc). The database permits access and downloads of all forms of data associated with any particular profile, including raw image files (.dat), processed image files (.cel), and interpretation files. We have also built a function in LIMS that simultaneously exports data to both the SQL web server, and the NCBI GEO database; the GEO files retain links back to the LIMS files. Finally, we have coded a gene-based cross-profile search function, that returns Avg Diff values for all profiles in the data warehouse, enabling rapid ascertainment of transcript levels in dozens of tissues and pathological conditions in mouse, rat, and human. PGA-CPR is available through http://microarray.cnmcresearch.org/pga.htm
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