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


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2014-10-14

AUTHORS

Brian D. Aevermann, Brett E. Pickett, Sanjeev Kumar, Edward B. Klem, Sudhakar Agnihothram, Peter S. Askovich, Armand Bankhead, Meagen Bolles, Victoria Carter, Jean Chang, Therese R.W. Clauss, Pradyot Dash, Alan H. Diercks, Amie J. Eisfeld, Amy Ellis, Shufang Fan, Martin T. Ferris, Lisa E. Gralinski, Richard R. Green, Marina A. Gritsenko, Masato Hatta, Robert A. Heegel, Jon M. Jacobs, Sophia Jeng, Laurence Josset, Shari M. Kaiser, Sara Kelly, G. Lynn Law, Chengjun Li, Jiangning Li, Casey Long, Maria L. Luna, Melissa Matzke, Jason McDermott, Vineet Menachery, Thomas O. Metz, Hugh Mitchell, Matthew E. Monroe, Garnet Navarro, Gabriele Neumann, Rebecca L. Podyminogin, Samuel O. Purvine, Carrie M. Rosenberger, Catherine J. Sanders, Athena A. Schepmoes, Anil K. Shukla, Amy Sims, Pavel Sova, Vincent C. Tam, Nicolas Tchitchek, Paul G. Thomas, Susan C. Tilton, Allison Totura, Jing Wang, Bobbie-Jo Webb-Robertson, Ji Wen, Jeffrey M. Weiss, Feng Yang, Boyd Yount, Qibin Zhang, Shannon McWeeney, Richard D. Smith, Katrina M. Waters, Yoshihiro Kawaoka, Ralph Baric, Alan Aderem, Michael G. Katze, Richard H. Scheuermann

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. More... »

PAGES

140033

References to SciGraph publications

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  • Journal

    TITLE

    Scientific Data

    ISSUE

    1

    VOLUME

    1

    Author Affiliations

  • J. Craig Venter Institute, 92037, La Jolla, CA, USA
  • Northrop Grumman Information Systems, Health IT, 20850, Rockville, MD, USA
  • Department of Epidemiology, University of North Carolina at Chapel Hill, 27599-7400, Chapel Hill, NC, USA
  • Seattle Biomedical Research Institute, 98109, Seattle, WA, USA
  • Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health Sciences University, 97239-3098, Portland, Oregon, USA
  • Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, 27599-7290, Chapel Hill, North Carolina, USA
  • Department of Microbiology, University of Washington, 98195, Seattle, WA, USA
  • Biological Sciences Division, Pacific Northwest National Laboratory, 99352, Richland, WA, USA
  • Department of Immunology, St. Jude Children’s Research Hospital, 38105-3678, Memphis, TN, USA
  • Department of Pathobiological Sciences Influenza Research Institute, School of Veterinary Medicine, Influenza Research Institute, University of Wisconsin-Madison, 53706, Madison, WI, USA
  • Department of Genetics, University of North Carolina at Chapel Hill, 27599-7264, Chapel Hill, NC, USA
  • Oregon Clinical & Translational Research Institute, 97239-3098, Portland, Oregon, USA
  • Present address: Kineta, Inc. 219 Terry Ave N Suite 300, Seattle, WA, USA
  • Division of Animal influenza, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 150001, Harbin, Heilongjiang Province, China
  • Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 99354, Richland, WA, USA
  • Present address: Diagnostic Discovery, Genentech, Inc., South San Francisco, CA, USA
  • Washington National Primate Research Center, University of Washington, 98195, Seattle, WA, USA
  • Department of Pathology, University of California, 92093, San Diego, CA, USA
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/sdata.2014.33

    DOI

    http://dx.doi.org/10.1038/sdata.2014.33

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1030429743

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/25977790


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