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

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). As a result, 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.
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  1. J. Craig Venter Institute, La Jolla, CA (United States)
  2. Northrop Grumman Information Systems, Rockville, MD (United States)
  3. Univ. of North Carolina, Chapel Hill, NC (United States)
  4. Seattle Biomedical Research Institute, Seattle, WA (United States)
  5. Oregon Clinical & Translational Research Institute, Portland, OR (United States); Oregon Health Sciences Univ., Portland, OR (United States)
  6. Univ. of Washington, Seattle, WA (United States)
  7. Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
  8. St. Jude Children's Research Hospital, Memphis, TN (United States)
  9. Univ. of Wisconsin-Madison, Madison, WI (United States)
  10. Oregon Clinical & Translational Research Institute, Portland, OR (United States)
  11. Chinese Academy of Agricultural Science, Heilongjiang Province (China)
  12. Seattle Biomedical Research Institute, Seattle, WA (United States); Genentech, Inc., South San Francisco, CA (United States)
  13. J. Craig Venter Institute, La Jolla, CA (United States); Univ. of California, San Diego, CA (United States)
Publication Date:
OSTI Identifier:
1167599
Report Number(s):
PNNL-SA--101269
Journal ID: ISSN 2052-4463; WN0219080
Grant/Contract Number:
AC05-76RL01830
Type:
Accepted Manuscript
Journal Name:
Scientific Data
Additional Journal Information:
Journal Volume: 1; Journal ID: ISSN 2052-4463
Publisher:
Nature Publishing Group
Research Org:
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES systems biology; proteomics; transcriptomics; data mining; databases; systems analysis; viral host response