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

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 & 48 others 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

Research output: Contribution to journalArticle

14 Citations (Scopus)

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.

Original languageEnglish (US)
Article number140033
JournalScientific data
Volume1
DOIs
StatePublished - Oct 14 2014
Externally publishedYes

Fingerprint

Pathogens
Systems Biology
Viruses
Virus
contagious disease
Infection
biology
Influenza
Infectious Diseases
Severe Acute Respiratory Syndrome
Allergies
Differential Expression
Proteomics
Quality Control
Metadata
RNA
Mutant
allergy
Repository
Quality control

ASJC Scopus subject areas

  • Statistics and Probability
  • Information Systems
  • Education
  • Computer Science Applications
  • Statistics, Probability and Uncertainty
  • Library and Information Sciences

Cite this

Aevermann, B. D., Pickett, B. E., Kumar, S., Klem, E. B., Agnihothram, S., Askovich, P. S., ... Scheuermann, R. H. (2014). A comprehensive collection of systems biology data characterizing the host response to viral infection. Scientific data, 1, [140033]. https://doi.org/10.1038/sdata.2014.33

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

In: Scientific data, Vol. 1, 140033, 14.10.2014.

Research output: Contribution to journalArticle

Aevermann, BD, Pickett, BE, Kumar, S, Klem, EB, Agnihothram, S, Askovich, PS, Bankhead, A, Bolles, M, Carter, V, Chang, J, Clauss, TRW, Dash, P, Diercks, AH, Eisfeld, AJ, Ellis, A, Fan, S, Ferris, MT, Gralinski, LE, Green, RR, Gritsenko, MA, Hatta, M, Heegel, RA, Jacobs, JM, Jeng, S, Josset, L, Kaiser, SM, Kelly, S, Law, GL, Li, C, Li, J, Long, C, Luna, ML, Matzke, M, McDermott, J, Menachery, V, Metz, TO, Mitchell, H, Monroe, ME, Navarro, G, Neumann, G, Podyminogin, RL, Purvine, SO, Rosenberger, CM, Sanders, CJ, Schepmoes, AA, Shukla, AK, Sims, A, Sova, P, Tam, VC, Tchitchek, N, Thomas, PG, Tilton, SC, Totura, A, Wang, J, Webb-Robertson, BJ, Wen, J, Weiss, JM, Yang, F, Yount, B, Zhang, Q, McWeeney, S, Smith, RD, Waters, KM, Kawaoka, Y, Baric, R, Aderem, A, Katze, MG & Scheuermann, RH 2014, 'A comprehensive collection of systems biology data characterizing the host response to viral infection', Scientific data, vol. 1, 140033. https://doi.org/10.1038/sdata.2014.33
Aevermann BD, Pickett BE, Kumar S, Klem EB, Agnihothram S, Askovich PS et al. A comprehensive collection of systems biology data characterizing the host response to viral infection. Scientific data. 2014 Oct 14;1. 140033. https://doi.org/10.1038/sdata.2014.33
Aevermann, Brian D. ; Pickett, Brett E. ; Kumar, Sanjeev ; Klem, Edward B. ; Agnihothram, Sudhakar ; Askovich, Peter S. ; Bankhead, Armand ; Bolles, Meagen ; Carter, Victoria ; Chang, Jean ; Clauss, Therese R.W. ; Dash, Pradyot ; Diercks, Alan H. ; Eisfeld, Amie J. ; Ellis, Amy ; Fan, Shufang ; Ferris, Martin T. ; Gralinski, Lisa E. ; Green, Richard R. ; Gritsenko, Marina A. ; Hatta, Masato ; Heegel, Robert A. ; Jacobs, Jon M. ; Jeng, Sophia ; Josset, Laurence ; Kaiser, Shari M. ; Kelly, Sara ; Law, G. Lynn ; Li, Chengjun ; Li, Jiangning ; Long, Casey ; Luna, Maria L. ; Matzke, Melissa ; McDermott, Jason ; Menachery, Vineet ; Metz, Thomas O. ; Mitchell, Hugh ; Monroe, Matthew E. ; Navarro, Garnet ; Neumann, Gabriele ; Podyminogin, Rebecca L. ; Purvine, Samuel O. ; Rosenberger, Carrie M. ; Sanders, Catherine J. ; Schepmoes, Athena A. ; Shukla, Anil K. ; Sims, Amy ; Sova, Pavel ; Tam, Vincent C. ; Tchitchek, Nicolas ; Thomas, Paul G. ; Tilton, Susan C. ; Totura, Allison ; Wang, Jing ; Webb-Robertson, Bobbie Jo ; Wen, Ji ; Weiss, Jeffrey M. ; Yang, Feng ; Yount, Boyd ; Zhang, Qibin ; McWeeney, Shannon ; Smith, Richard D. ; Waters, Katrina M. ; Kawaoka, Yoshihiro ; Baric, Ralph ; Aderem, Alan ; Katze, Michael G. ; Scheuermann, Richard H. / A comprehensive collection of systems biology data characterizing the host response to viral infection. In: Scientific data. 2014 ; Vol. 1.
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