Database Implementation and Data Analysis

Integrated data management is achieved through different levels of support that follows any given project from “soup to nuts”. For this, we have designed the Public Expression Profiling Resource (PEPR), a second generation web Oracle database that provides a streamlined, integrated workflow process of proposal submission, data generation/interpretation, expression profile publishing and data visualization. PEPR allows remote users to submit and track samples, and enter and edit sample meta data. PEPR is designed to provide seamless “single button” transition of projects from “private remote” access to “public access”, including through pre-existing automated pipelines into NCBI GEO. Furthermore, through PEPR, public users of the data can perform intuitive and simple mining of large microarray datasets and associated meta data, which requires no prior knowledge of microarray methods or data analyses. PEPR is one of only a handful of dynamic query resources for massively parallel and multi-dimensional biological datasets that are publicly available.

For analysis, we have developed our own highly popular clustering program, Hierarchical Cluster Explorer (HCE), for dissemination to core users. This software is provided with training and helpdesk functions. In addition to HCE, many popular analysis packages (including a network version of Pathway Assist for biochemical pathway evaluation) are also available. The analysis tool for each particular project and research question is selected through discussion with our informatics and statistics consultants.

We tailor the level of database and/or analysis support to each investigator, to provide individualized solutions for the needed level of assistance. The fee schedule for database implementation depends upon the amount of support required for a given project. Assistance with data analysis is free of charge. Please contact Eric Hoffman (ehoffman@cnmcresearch.org or (202) 884-6029) or Susan Knoblach (sknoblach@cnmcresearch.org or (202) 884-6094) to discuss price schedules.