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PEPR Portal

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PEPR is Under Re-Construction!

Please contact the system administrator if you experience any difficulties during this period.

Welcome to the Public Expression Profiling Resource (PEPR).

PEPR is an experiment in web-database access to large multi-dimensional data sets using a standardized experimental platform.

The primary goal of PEPR is to determine if the larger scientific community can be given simple, intuitive, and user-friendly web-based access to large microarray data sets. Note that all data in PEPR is also available via NCBI GEO.

The structure and goals of PEPR differ from other mRNA expression profiling databases in a number of important ways.

  • The experimental platform in PEPR is standardized, and is an Affymetrix -only database . All microarrays available in the PEPR web database should ascribe to quality control and standard operating procedures. A recent publication has described the QC/SOP criteria utilized in PEPR profiles ( The Tumor Analysis Best Practices Working Group 2004 ).
  • PEPR permits gene-based queries of large Affymetrix array data sets without any specialized software. For example, a number of large time series projects are available within PEPR, containing 40-60 microarrays, yet these can be simply queried via a dynamic web interface with no prior knowledge of microarray data analysis.
  • Projects in PEPR originate from scientists world-wide, but all data has been generated by the Research Center for Genetic Medicine, Children's National Medical Center, Washington DC . Future developments of PEPR will allow remote entry of Affymetrix data ascribing to the same QC/SOP protocols. We have previously described an initial implementation of PEPR, and a dynamic web-queried time series graphical interface ( Chen et al. 2004 ). A publication showing the utility of PEPR for pharmacodynamic data has recently been published ( Almon et al. 2003 ).

You are now using the second generation implementation of PEPR .

For a description of the initial implementation of PEPR, and what we learned from this, please see Background (PEPR v. 1).

For a description of the design and implemention of this current second generation of PEPR, please see Design Goals (PEPR v. 2).

To take advantage of the full spectrum of services offered by the PEPR, please register now.

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