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Database (2009) Vol. 2009:bap011; doi:10.1093/database/bap011 published on September 17, 2009
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© The Author(s) 2009. Published by Oxford University Press.
This is Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

The Prion Disease Database: a comprehensive transcriptome resource for systems biology research in prion diseases

Nils Gehlenborg1,2, Daehee Hwang1,3, Inyoul Y. Lee1, Hyuntae Yoo1, David Baxter1, Brianne Petritis1, Rose Pitstick4, Bruz Marzolf1, Stephen J. DeArmond5, George A. Carlson4,* and Leroy Hood1,*

1Institute for Systems Biology, Seattle, WA 98103, USA, 2European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK, 3I-Bio Program & Department of Chemical Engineering, POSTECH, Pohang, 790-784, Republic of Korea, 4McLaughlin Research Institute, Great Falls, MT 59405 and 5Department of Pathology, University of California, San Francisco, CA 94158, USA

*Corresponding author: Tel: +1 206 732 1201; Fax: +1 206 732 1299; Email: lhood{at}systemsbiology.org Correspondence may also be addressed to George A. Carlson. Tel: +1 406 452 6208; Fax: +1 406 454 6019; Email: gac{at}po.mri.montana.edu


  Abstract

Prion diseases reflect conformational conversion of benign isoforms of prion protein (PrPC) to malignant PrPSc isoforms. Networks perturbed by PrPSc accumulation and their ties to pathological events are poorly understood. Time-course transcriptomic and phenotypic data in animal models are critical for understanding prion-perturbed networks in systems biology studies. Here, we present the Prion Disease Database (PDDB), the most comprehensive data resource on mouse prion diseases to date. The PDDB contains: (i) time-course mRNA measurements spanning the interval from prion inoculation through appearance of clinical signs in eight mouse strain-prion strain combinations and (ii) histoblots showing temporal PrPSc accumulation patterns in brains from each mouse–prion combination. To facilitate prion research, the PDDB also provides a suite of analytical tools for reconstructing dynamic networks via integration of temporal mRNA and interaction data and for analyzing these networks to generate hypotheses.

Database URL: http://prion.systemsbiology.net

Received May 10, 2009; Revised July 17, 2009; Accepted August 11, 2009


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