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

Database

Volumn 2009, Issue , 2009, Pages

  Gehlenborg, Nils ^a,b   Hwang, Daehee ^a,c   Lee, Inyoul Y ^a   Yoo, Hyuntae ^a   Baxter, David ^a   Petritis, Brianne ^a   Pitstick, Rose ^d   Marzolf, Bruz ^a   DeArmond, Stephen J ^e   Carlson, George A ^d   Hood, Leroy ^a  

^a INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^c Pohang University of Science and Technology (POSTECH)   (South Korea)

^d MCLAUGHLIN RESEARCH INSTITUTE   (United States)

^e UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84908106285     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/bap011     Document Type: Article

References (27)

1. Hood, L., Heath, J.R., Phelps, M.E. et al. (2004) Systems biology and new technologies enable predictive and preventative medicine. Science, 306, 640-643.
2. Lin, B., White, J.T., Lu, W. et al. (2005) Evidence for the presence of disease-perturbed networks in prostate cancer cells by genomic and proteomic analyses: a systems approach to disease. Cancer Res., 65, 3081-3091.
3. Price, N.D., Edelman, L., Lee, I. et al. (2009) Systems biology and the emergence of systems medicine. In Willard, H.F. and Ginsburg, G.S. (eds), Genomic and Personalized Medicine: From Principles to Practice. New York, Academic Press, Vol. I, pp. 74-85.
4. Prusiner, S.B. (1998) Prions. Proc. Natl Acad. Sci. USA, 95, 13363-13383.
5. Prusiner, S.B. (2003) Prion Biology and Diseases. 2nd edn, Cold Spring Harbor Laboratory Press, pp. 1-88.
6. Skinner, P.J., Abbassi, H., Chesebro, B. et al. (2006) Gene expression alterations in brains of mice infected with three strains of scrapie. BMC Genomics, 7, 114.
7. Sorensen, G., Medina, S., Parchaliuk, D. et al. (2008) Comprehensive transcriptional profiling of prion infection in mouse models reveals networks of responsive genes. BMC Genomics, 9, 114.
8. Xiang, W., Hummel, M., Mitteregger, G. et al. (2007) Transcriptome analysis reveals altered cholesterol metabolism during the neurodegeneration in mouse scrapie model. J. Neurochem., 102, 834-847.
9. Hwang, D., Lee, I.Y., Yoo, H. et al. (2009) A systems approach to prion disease. Mol. Syst. Biol., 5, 252.
10. Bertram, L., McQueen, M.B., Mullin, K. et al. (2007) Systematic meta-analyses of Alzheimer disease genetic association studies: the AlzGene database. Nat. Genet., 39, 17-23.
11. Goodman, N. (2009) HDBase - a community website for Huntington's disease research. http://www.hdbase.org.
12. Bagade, S., Allen, N.C., Tanzi, R.E. et al. (2009) The PDGene Database. http://www.pdgene.org.
13. Shannon, P.T., Reiss, D.J., Bonneau, R. et al. (2006) The Gaggle: an open-source software system for integrating bioinformatics software and data sources. BMC Bioinformatics, 7, 176.
14. Smink, L.J., Helton, E.M., Healy, B.C. et al. (2005) T1DBase, a community web-based resource for type 1 diabetes research. Nucleic Acids Res., 33, D544-D549.
15. Bare, J.C., Shannon, P.T., Schmid, A.K. et al. (2007) The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications. BMC Bioinformatics, 8, 456.
16. Shannon, P., Markiel, A., Ozier, O. et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res., 13, 2498-2504.
17. Longabaugh, W.J., Davidson, E.H. and Bolouri, H. (2005) Computational representation of developmental genetic regulatory networks. Dev. Biol., 283, 1-16.
18. Dennis, G. Jr., Sherman, B.T., Hosack, D.A. et al. (2003) DAVID: database for annotation, visualization, and integrated discovery. Genome Biol., 4, P3.
19. Dietzsch, J., Gehlenborg, N. and Nieselt, K. (2006) Mayday-a microarray data analysis workbench. Bioinformatics, 22, 1010-1012.
20. Gehlenborg, N., Yan, W., Lee, I.Y. et al. (2009) Prequips-an extensible software platform for integration, visualization and analysis of LC-MS/MS proteomics data. Bioinformatics, 25, 682-683.
21. Gilchrist, M., Thorsson, V., Li, B. et al. (2006) Systems biology approaches identify ATF3 as a negative regulator of Toll-like receptor 4. Nature, 441, 173-178.
22. Cerami, E.G., Bader, G.D., Gross, B.E. et al. (2006) cPath: open source software for collecting, storing, and querying biological pathways. BMC Bioinformatics, 7, 497.
23. Jayapandian, M., Chapman, A., Tarcea, V.G. et al. (2007) Michigan molecular interactions (MiMI): putting the jigsaw puzzle together. Nucleic Acids Res., 35, D566-D571.
24. Maere, S., Heymans, K. and Kuiper, M. (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics, 21, 3448-3449.
25. Ideker, T., Ozier, O., Schwikowski, B. et al. (2002) Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics, 18 (Suppl. 1), S233-S240.
26. Saeed, A.I., Sharov, V., White, J. et al. (2003) TM4: a free, opensource system for microarray data management and analysis. Biotechniques, 34, 374-378.
27. Huminiecki, L., Lloyd, A.T. and Wolfe, K.H. (2003) Congruence of tissue expression profiles from Gene Expression Atlas, SAGEmap and TissueInfo databases. BMC Genomics, 4, 31.