InnateDB: Facilitating systems-level analyses of the mammalian innate immune response

David J. Lynn, Geoffrey L. Winsor, Calvin Chan, Nicolas Richard, Matthew R. Laird, Aaron Barsky, Jennifer L. Gardy, Fiona M. Roche, Timothy H W Chan, Naisha Shah, Raymond Lo, Misbah Naseer, Jaimmie Que, Melissa Yau, Michael Acab, Dan Tulpan, Matthew D. Whiteside, Avinash Chikatamarla, Bernadette Mah, Tamara Munzner & 3 others Karsten Hokamp, Robert E W Hancock, Fiona S L Brinkman

Research output: Contribution to journalArticle

261 Citations (Scopus)

Abstract

Although considerable progress has been made in dissecting the signaling pathways involved in the innate immune response, it is now apparent that this response can no longer be productively thought of in terms of simple linear pathways. InnateDB (www.innatedb.ca) has been developed to facilitate systems-level analyses that will provide better insight into the complex networks of pathways and interactions that govern the innate immune response. InnateDB is a publicly available, manually curated, integrative biology database of the human and mouse molecules, experimentally verified interactions and pathways involved in innate immunity, along with centralized annotation on the broader human and mouse interactomes. To date, more than 3500 innate immunity-relevant interactions have been contextually annotated through the review of 1000 plus publications. Integrated into InnateDB are novel bioinformatics resources, including network visualization software, pathway analysis, orthologous interaction network construction and the ability to overlay user-supplied gene expression data in an intuitively displayed molecular interaction network and pathway context, which will enable biologists without a computational background to explore their data in a more systems-oriented manner.

LanguageEnglish
Article number218
JournalMolecular Systems Biology
Volume4
DOIs
Publication statusPublished - 10 Sep 2008

Keywords

  • Database
  • Gene expression
  • Innate immunity
  • Interaction network
  • Pathway visualization

ASJC Scopus subject areas

  • Information Systems
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)
  • Agricultural and Biological Sciences(all)
  • Computational Theory and Mathematics
  • Applied Mathematics

Cite this

Lynn, D. J., Winsor, G. L., Chan, C., Richard, N., Laird, M. R., Barsky, A., ... Brinkman, F. S. L. (2008). InnateDB: Facilitating systems-level analyses of the mammalian innate immune response. Molecular Systems Biology, 4, [218]. https://doi.org/10.1038/msb.2008.55
Lynn, David J. ; Winsor, Geoffrey L. ; Chan, Calvin ; Richard, Nicolas ; Laird, Matthew R. ; Barsky, Aaron ; Gardy, Jennifer L. ; Roche, Fiona M. ; Chan, Timothy H W ; Shah, Naisha ; Lo, Raymond ; Naseer, Misbah ; Que, Jaimmie ; Yau, Melissa ; Acab, Michael ; Tulpan, Dan ; Whiteside, Matthew D. ; Chikatamarla, Avinash ; Mah, Bernadette ; Munzner, Tamara ; Hokamp, Karsten ; Hancock, Robert E W ; Brinkman, Fiona S L. / InnateDB : Facilitating systems-level analyses of the mammalian innate immune response. In: Molecular Systems Biology. 2008 ; Vol. 4.
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abstract = "Although considerable progress has been made in dissecting the signaling pathways involved in the innate immune response, it is now apparent that this response can no longer be productively thought of in terms of simple linear pathways. InnateDB (www.innatedb.ca) has been developed to facilitate systems-level analyses that will provide better insight into the complex networks of pathways and interactions that govern the innate immune response. InnateDB is a publicly available, manually curated, integrative biology database of the human and mouse molecules, experimentally verified interactions and pathways involved in innate immunity, along with centralized annotation on the broader human and mouse interactomes. To date, more than 3500 innate immunity-relevant interactions have been contextually annotated through the review of 1000 plus publications. Integrated into InnateDB are novel bioinformatics resources, including network visualization software, pathway analysis, orthologous interaction network construction and the ability to overlay user-supplied gene expression data in an intuitively displayed molecular interaction network and pathway context, which will enable biologists without a computational background to explore their data in a more systems-oriented manner.",
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Lynn, DJ, Winsor, GL, Chan, C, Richard, N, Laird, MR, Barsky, A, Gardy, JL, Roche, FM, Chan, THW, Shah, N, Lo, R, Naseer, M, Que, J, Yau, M, Acab, M, Tulpan, D, Whiteside, MD, Chikatamarla, A, Mah, B, Munzner, T, Hokamp, K, Hancock, REW & Brinkman, FSL 2008, 'InnateDB: Facilitating systems-level analyses of the mammalian innate immune response', Molecular Systems Biology, vol. 4, 218. https://doi.org/10.1038/msb.2008.55

InnateDB : Facilitating systems-level analyses of the mammalian innate immune response. / Lynn, David J.; Winsor, Geoffrey L.; Chan, Calvin; Richard, Nicolas; Laird, Matthew R.; Barsky, Aaron; Gardy, Jennifer L.; Roche, Fiona M.; Chan, Timothy H W; Shah, Naisha; Lo, Raymond; Naseer, Misbah; Que, Jaimmie; Yau, Melissa; Acab, Michael; Tulpan, Dan; Whiteside, Matthew D.; Chikatamarla, Avinash; Mah, Bernadette; Munzner, Tamara; Hokamp, Karsten; Hancock, Robert E W; Brinkman, Fiona S L.

In: Molecular Systems Biology, Vol. 4, 218, 10.09.2008.

Research output: Contribution to journalArticle

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AU - Winsor, Geoffrey L.

AU - Chan, Calvin

AU - Richard, Nicolas

AU - Laird, Matthew R.

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AU - Chan, Timothy H W

AU - Shah, Naisha

AU - Lo, Raymond

AU - Naseer, Misbah

AU - Que, Jaimmie

AU - Yau, Melissa

AU - Acab, Michael

AU - Tulpan, Dan

AU - Whiteside, Matthew D.

AU - Chikatamarla, Avinash

AU - Mah, Bernadette

AU - Munzner, Tamara

AU - Hokamp, Karsten

AU - Hancock, Robert E W

AU - Brinkman, Fiona S L

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