title: A comprehensive collection of systems biology data characterizing the host response to viral infection.
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.
authors.affiliation: J. Craig Venter Institute , La Jolla, CA 92037, USA.
authors.forename: Brian D
authors.initials: BD
authors.lastname: Aevermann
authors.affiliation: J. Craig Venter Institute , La Jolla, CA 92037, USA.
authors.forename: Brett E
authors.initials: BE
authors.lastname: Pickett
authors.affiliation: Northrop Grumman Information Systems, Health IT , Rockville, MD 20850, USA.
authors.forename: Sanjeev
authors.initials: S
authors.lastname: Kumar
authors.affiliation: Northrop Grumman Information Systems, Health IT , Rockville, MD 20850, USA.
authors.forename: Edward B
authors.initials: EB
authors.lastname: Klem
authors.affiliation: Department of Epidemiology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7400, USA.
authors.forename: Sudhakar
authors.initials: S
authors.lastname: Agnihothram
authors.affiliation: Seattle Biomedical Research Institute , Seattle, WA 98109, USA.
authors.forename: Peter S
authors.initials: PS
authors.lastname: Askovich
authors.affiliation: 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.
authors.forename: Armand
authors.initials: A
authors.lastname: Bankhead
authors.affiliation: Department of Microbiology and Immunology, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7290, USA.
authors.forename: Meagen
authors.initials: M
authors.lastname: Bolles
authors.affiliation: Department of Microbiology, University of Washington , Seattle, WA 98195, USA.
authors.forename: Victoria
authors.initials: V
authors.lastname: Carter
authors.affiliation: Department of Microbiology, University of Washington , Seattle, WA 98195, USA.
authors.forename: Jean
authors.initials: J
authors.lastname: Chang
authors.affiliation: Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA.
authors.forename: Therese R W
authors.initials: TR
authors.lastname: Clauss
authors.affiliation: Department of Immunology, St. Jude Children's Research Hospital , Memphis, TN 38105-3678, USA.
authors.forename: Pradyot
authors.initials: P
authors.lastname: Dash
authors.affiliation: Seattle Biomedical Research Institute , Seattle, WA 98109, USA.
authors.forename: Alan H
authors.initials: AH
authors.lastname: Diercks
authors.affiliation: School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison , Madison, WI 53706, USA.
authors.forename: Amie J
authors.initials: AJ
authors.lastname: Eisfeld
authors.affiliation: School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison , Madison, WI 53706, USA.
authors.forename: Amy
authors.initials: A
authors.lastname: Ellis
authors.affiliation: School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison , Madison, WI 53706, USA.
authors.forename: Shufang
authors.initials: S
authors.lastname: Fan
authors.affiliation: Department of Genetics, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7264, USA.
authors.forename: Martin T
authors.initials: MT
authors.lastname: Ferris
authors.affiliation: Department of Microbiology and Immunology, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7290, USA.
authors.forename: Lisa E
authors.initials: LE
authors.lastname: Gralinski
authors.affiliation: Department of Microbiology, University of Washington , Seattle, WA 98195, USA.
authors.forename: Richard R
authors.initials: RR
authors.lastname: Green
authors.affiliation: Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA.
authors.forename: Marina A
authors.initials: MA
authors.lastname: Gritsenko
authors.affiliation: School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison , Madison, WI 53706, USA.
authors.forename: Masato
authors.initials: M
authors.lastname: Hatta
authors.affiliation: Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA.
authors.forename: Robert A
authors.initials: RA
authors.lastname: Heegel
authors.affiliation: Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA.
authors.forename: Jon M
authors.initials: JM
authors.lastname: Jacobs
authors.affiliation: Oregon Clinical & Translational Research Institute , Portland, Oregon 97239-3098, USA.
authors.forename: Sophia
authors.initials: S
authors.lastname: Jeng
authors.affiliation: Department of Microbiology, University of Washington , Seattle, WA 98195, USA.
authors.forename: Laurence
authors.initials: L
authors.lastname: Josset
authors.affiliation: Seattle Biomedical Research Institute , Seattle, WA 98109, USA.
authors.forename: Shari M
authors.initials: SM
authors.lastname: Kaiser
authors.affiliation: Department of Microbiology, University of Washington , Seattle, WA 98195, USA.
authors.forename: Sara
authors.initials: S
authors.lastname: Kelly
authors.affiliation: Department of Microbiology, University of Washington , Seattle, WA 98195, USA.
authors.forename: G Lynn
authors.initials: GL
authors.lastname: Law
authors.affiliation: Division of Animal influenza, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences , Harbin, Heilongjiang Province 150001, China.
authors.forename: Chengjun
authors.initials: C
authors.lastname: Li
authors.affiliation: Seattle Biomedical Research Institute , Seattle, WA 98109, USA.
authors.forename: Jiangning
authors.initials: J
authors.lastname: Li
authors.affiliation: Department of Epidemiology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7400, USA.
authors.forename: Casey
authors.initials: C
authors.lastname: Long
authors.affiliation: Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA.
authors.forename: Maria L
authors.initials: ML
authors.lastname: Luna
authors.affiliation: Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA.
authors.forename: Melissa
authors.initials: M
authors.lastname: Matzke
authors.affiliation: Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA.
authors.forename: Jason
authors.initials: J
authors.lastname: McDermott
authors.affiliation: Department of Epidemiology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7400, USA.
authors.forename: Vineet
authors.initials: V
authors.lastname: Menachery
authors.affiliation: Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA.
authors.forename: Thomas O
authors.initials: TO
authors.lastname: Metz
authors.affiliation: Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA.
authors.forename: Hugh
authors.initials: H
authors.lastname: Mitchell
authors.affiliation: Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA.
authors.forename: Matthew E
authors.initials: ME
authors.lastname: Monroe
authors.affiliation: Seattle Biomedical Research Institute , Seattle, WA 98109, USA.
authors.forename: Garnet
authors.initials: G
authors.lastname: Navarro
authors.affiliation: School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison , Madison, WI 53706, USA.
authors.forename: Gabriele
authors.initials: G
authors.lastname: Neumann
authors.affiliation: Seattle Biomedical Research Institute , Seattle, WA 98109, USA.
authors.forename: Rebecca L
authors.initials: RL
authors.lastname: Podyminogin
authors.affiliation: Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory , Richland, WA 99354, USA.
authors.forename: Samuel O
authors.initials: SO
authors.lastname: Purvine
authors.affiliation: Seattle Biomedical Research Institute , Seattle, WA 98109, USA.
authors.forename: Carrie M
authors.initials: CM
authors.lastname: Rosenberger
authors.affiliation: Department of Immunology, St. Jude Children's Research Hospital , Memphis, TN 38105-3678, USA.
authors.forename: Catherine J
authors.initials: CJ
authors.lastname: Sanders
authors.affiliation: Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA.
authors.forename: Athena A
authors.initials: AA
authors.lastname: Schepmoes
authors.affiliation: Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA.
authors.forename: Anil K
authors.initials: AK
authors.lastname: Shukla
authors.affiliation: Department of Epidemiology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7400, USA.
authors.forename: Amy
authors.initials: A
authors.lastname: Sims
authors.affiliation: Department of Microbiology, University of Washington , Seattle, WA 98195, USA.
authors.forename: Pavel
authors.initials: P
authors.lastname: Sova
authors.affiliation: Seattle Biomedical Research Institute , Seattle, WA 98109, USA.
authors.forename: Vincent C
authors.initials: VC
authors.lastname: Tam
authors.affiliation: Department of Microbiology, University of Washington , Seattle, WA 98195, USA.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Tchitchek
authors.affiliation: Department of Immunology, St. Jude Children's Research Hospital , Memphis, TN 38105-3678, USA.
authors.forename: Paul G
authors.initials: PG
authors.lastname: Thomas
authors.affiliation: Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA.
authors.forename: Susan C
authors.initials: SC
authors.lastname: Tilton
authors.affiliation: Department of Microbiology and Immunology, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7290, USA.
authors.forename: Allison
authors.initials: A
authors.lastname: Totura
authors.affiliation: Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA.
authors.forename: Jing
authors.initials: J
authors.lastname: Wang
authors.affiliation: Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA.
authors.forename: Bobbie-Jo
authors.initials: BJ
authors.lastname: Webb-Robertson
authors.affiliation: Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA.
authors.forename: Ji
authors.initials: J
authors.lastname: Wen
authors.affiliation: Department of Microbiology, University of Washington , Seattle, WA 98195, USA.
authors.forename: Jeffrey M
authors.initials: JM
authors.lastname: Weiss
authors.affiliation: Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA.
authors.forename: Feng
authors.initials: F
authors.lastname: Yang
authors.affiliation: Department of Epidemiology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7400, USA.
authors.forename: Boyd
authors.initials: B
authors.lastname: Yount
authors.affiliation: Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA.
authors.forename: Qibin
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: 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.
authors.forename: Shannon
authors.initials: S
authors.lastname: McWeeney
authors.affiliation: Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA.
authors.forename: Richard D
authors.initials: RD
authors.lastname: Smith
authors.affiliation: Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA.
authors.forename: Katrina M
authors.initials: KM
authors.lastname: Waters
authors.affiliation: School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison , Madison, WI 53706, USA.
authors.forename: Yoshihiro
authors.initials: Y
authors.lastname: Kawaoka
authors.affiliation: 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.
authors.forename: Ralph
authors.initials: R
authors.lastname: Baric
authors.affiliation: Seattle Biomedical Research Institute , Seattle, WA 98109, USA.
authors.forename: Alan
authors.initials: A
authors.lastname: Aderem
authors.affiliation: Department of Microbiology, University of Washington , Seattle, WA 98195, USA ; Washington National Primate Research Center, University of Washington , Seattle, WA 98195, USA.
authors.forename: Michael G
authors.initials: MG
authors.lastname: Katze
authors.affiliation: J. Craig Venter Institute , La Jolla, CA 92037, USA ; Department of Pathology, University of California , San Diego, CA 92093, USA.
authors.forename: Richard H
authors.initials: RH
authors.lastname: Scheuermann
mesh_terms: D000818:Animals; D003625:Data Collection; D016208:Databases, Factual; D054884:Host-Pathogen Interactions; D006801:Humans; D009980:Influenza A virus / Q000472:pathogenicity / Q000502:physiology; D007251:Influenza, Human / Q000503:physiopathology / Q000821:virology*; D051379:Mice; D009976:Orthomyxoviridae Infections / Q000503:physiopathology / Q000821:virology*; D049490:Systems Biology