The Oral Pathogen Microarray Database

Objective: The completion of several genome-sequencing projects for oral pathogens has made genome-wide gene expression studies possible using DNA microarrays. Microarray data usually contain thousands of data points that are difficult to analyze and interpret. The Oral Pathogen Microarray Database (OPMD) provides tools and databases that are specifically designed to analyze, view, store and share microarray information generated from studies on oral pathogens. Method: The database was constructed based on the open source database Longhorn Array Database (LAD) that operates on PostgreSQL and Linux. Analysis tools were developed with the combination of several programming languages: R, Perl and PHP. Results: A publicly accessible microarray database was created and can be used for storing both raw and normalized two-color array data, as well as the corresponding image files. The database also provides interfaces for data retrieval, analysis, and visualization, as well as web links for each array spot to the corresponding gene feature in a graphical genome viewer. Registered users can upload data for private or public purposes. Data that have been referred in publications can be made publicly accessible and are compliant to the "Minimum Information About a Microarray Experiment " (MIAME) standard. An easy-to-use tool "Significance Analysis of Oral Pathogen Microarray Data" (SAOPMD) was also designed to perform statistical analysis for custom-uploaded data. SAOPMD features advanced normalization algorithms and statistics functions to evaluate the biological significance of the data. Currently SAOPMD accepts two-color microarray data from both versions of Porphyromonas gingivalis slides made by The Institute for Genomic Research (TIGR). Other formats can be accepted upon request. Conclusion: OPMD is specifically designed for oral / dental research community and serves as a public repository for oral pathogen microarray data. OPMD can be accessed at http://array.brop.org. Supported by NIDCR K22 DE14742.