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Sci Data. 2014 Oct 14;1:140033. doi: 10.1038/sdata.2014.33. eCollection 2014.

A comprehensive collection of systems biology data characterizing the host response to viral infection.

Author information

1
J. Craig Venter Institute , La Jolla, CA 92037, USA.
2
Northrop Grumman Information Systems, Health IT , Rockville, MD 20850, USA.
3
Department of Epidemiology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7400, USA.
4
Seattle Biomedical Research Institute , Seattle, WA 98109, USA.
5
Oregon Clinical & Translational Research Institute , Portland, Oregon 97239-3098, USA ; Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health Sciences University , Portland, Oregon 97239-3098, USA.
6
Department of Microbiology and Immunology, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7290, USA.
7
Department of Microbiology, University of Washington , Seattle, WA 98195, USA.
8
Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA.
9
Department of Immunology, St. Jude Children's Research Hospital , Memphis, TN 38105-3678, USA.
10
School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison , Madison, WI 53706, USA.
11
Department of Genetics, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7264, USA.
12
Oregon Clinical & Translational Research Institute , Portland, Oregon 97239-3098, USA.
13
Division of Animal influenza, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences , Harbin, Heilongjiang Province 150001, China.
14
Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory , Richland, WA 99354, USA.
15
Department of Epidemiology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7400, USA ; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7290, USA.
16
Department of Microbiology, University of Washington , Seattle, WA 98195, USA ; Washington National Primate Research Center, University of Washington , Seattle, WA 98195, USA.
17
J. Craig Venter Institute , La Jolla, CA 92037, USA ; Department of Pathology, University of California , San Diego, CA 92093, USA.

Abstract

The Systems Biology for Infectious Diseases Research program was established by the U.S. National Institute of Allergy and Infectious Diseases to investigate host-pathogen interactions at a systems level. This program generated 47 transcriptomic and proteomic datasets from 30 studies that investigate in vivo and in vitro host responses to viral infections. Human pathogens in the Orthomyxoviridae and Coronaviridae families, especially pandemic H1N1 and avian H5N1 influenza A viruses and severe acute respiratory syndrome coronavirus (SARS-CoV), were investigated. Study validation was demonstrated via experimental quality control measures and meta-analysis of independent experiments performed under similar conditions. Primary assay results are archived at the GEO and PeptideAtlas public repositories, while processed statistical results together with standardized metadata are publically available at the Influenza Research Database (www.fludb.org) and the Virus Pathogen Resource (www.viprbrc.org). By comparing data from mutant versus wild-type virus and host strains, RNA versus protein differential expression, and infection with genetically similar strains, these data can be used to further investigate genetic and physiological determinants of host responses to viral infection.

PMID:
25977790
PMCID:
PMC4410982
DOI:
10.1038/sdata.2014.33
[Indexed for MEDLINE]
Free PMC Article

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