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

Journal Article · · Scientific Data
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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)
+ Show Author Affiliations
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.
Research Organization:
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Grant/Contract Number:
AC05-76RL01830
OSTI ID:
1167599
Report Number(s):
PNNL-SA--101269; WN0219080
Journal Information:
Scientific Data, Journal Name: Scientific Data Vol. 1; ISSN 2052-4463
Publisher:
Nature Publishing GroupCopyright Statement
Country of Publication:
United States
Language:
English

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Severe Acute Respiratory Syndrome Coronavirus Group-Specific Open Reading Frames Encode Nonessential Functions for Replication in Cell Cultures and Mice text January 2005
Improved quality control processing of peptide-centric LC-MS proteomics data text January 2011
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  • E., Gralinski, Lisa; Sudhakar, Agnihothram,; S., Carter, Victoria
  • The University of North Carolina at Chapel Hill University Libraries https://doi.org/10.17615/mdjq-3337
text January 2013
Synthetic recombinant bat SARS-like coronavirus is infectious in cultured cells and in mice text January 2008
Mechanisms of Severe Acute Respiratory Syndrome Coronavirus-Induced Acute Lung Injury text January 2013

Cited By (44)

MERS-CoV and H5N1 influenza virus antagonize antigen presentation by altering the epigenetic landscape journal January 2018
Annotating Protein Functional Residues by Coupling High-Throughput Fitness Profile and Homologous-Structure Analysis journal December 2016
Integrating Transcriptomic and Proteomic Data Using Predictive Regulatory Network Models of Host Response to Pathogens journal July 2016
Unified feature association networks through integration of transcriptomic and proteomic data journal September 2019
Influenza Research Database: An integrated bioinformatics resource for influenza virus research text January 2017
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Epigenetic Landscape during Coronavirus Infection journal February 2017
A transcriptional regulatory atlas of coronavirus infection of human cells collection January 2020
The landscape of viral proteomics and its potential to impact human health journal May 2016
Influenza Research Database: An integrated bioinformatics resource for influenza virus research journal September 2016
Extracting allelic read counts from 250,000 human sequencing runs in Sequence Read Archive posted_content August 2018
EMBL2checklists: A Python package to facilitate the user-friendly submission of plant DNA barcoding sequences to ENA journal October 2018
Extracting allelic read counts from 250,000 human sequencing runs in Sequence Read Archive conference November 2018
Myeloid TBK1 Signaling Contributes to the Immune Response to Influenza journal March 2019
Myeloid TBK1 signaling contributes to the immune response to influenza text January 2019
MERS-CoV and H5N1 influenza virus antagonize antigen presentation by altering the epigenetic landscape
  • M., Webb-Robertson, Bobbie-Jo; D., Nicora, Carrie; O., Metz, Thomas
  • The University of North Carolina at Chapel Hill University Libraries https://doi.org/10.17615/t9e6-8v94
text January 2018
Unified feature association networks through integration of transcriptomic and proteomic data
  • P., Wendler, Jason; L., Deatherage Kaiser, Brooke; Kristie, Oxford,
  • The University of North Carolina at Chapel Hill University Libraries https://doi.org/10.17615/z5gg-x726
text January 2019

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59 BASIC BIOLOGICAL SCIENCES
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