Curating the innate immunity interactome

David J. Lynn, Calvin Chan, Misbah Naseer, Melissa Yau, Raymond Lo, Anastasia Sribnaia, Giselle Ring, Jaimmie Que, Kathleen Wee, Geoffrey L. Winsor, Matthew R. Laird, Karin Breuer, Amir K. Foroushani, Fiona S L Brinkman, Robert E W Hancock

Research output: Contribution to journalArticle

57 Citations (Scopus)

Abstract

Background: The innate immune response is the first line of defence against invading pathogens and is regulated by complex signalling and transcriptional networks. Systems biology approaches promise to shed new light on the regulation of innate immunity through the analysis and modelling of these networks. A key initial step in this process is the contextual cataloguing of the components of this system and the molecular interactions that comprise these networks. InnateDB (http://www.innatedb.com) is a molecular interaction and pathway database developed to facilitate systems-level analyses of innate immunity.Results: Here, we describe the InnateDB curation project, which is manually annotating the human and mouse innate immunity interactome in rich contextual detail, and present our novel curation software system, which has been developed to ensure interactions are curated in a highly accurate and data-standards compliant manner. To date, over 13,000 interactions (protein, DNA and RNA) have been curated from the biomedical literature. Here, we present data, illustrating how InnateDB curation of the innate immunity interactome has greatly enhanced network and pathway annotation available for systems-level analysis and discuss the challenges that face such curation efforts. Significantly, we provide several lines of evidence that analysis of the innate immunity interactome has the potential to identify novel signalling, transcriptional and post-transcriptional regulators of innate immunity. Additionally, these analyses also provide insight into the cross-talk between innate immunity pathways and other biological processes, such as adaptive immunity, cancer and diabetes, and intriguingly, suggests links to other pathways, which as yet, have not been implicated in the innate immune response.Conclusions: In summary, curation of the InnateDB interactome provides a wealth of information to enable systems-level analysis of innate immunity.

LanguageEnglish
Article number117
JournalBMC Systems Biology
Volume4
DOIs
Publication statusPublished - 20 Aug 2010

ASJC Scopus subject areas

  • Structural Biology
  • Modelling and Simulation
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics

Cite this

Lynn, D. J., Chan, C., Naseer, M., Yau, M., Lo, R., Sribnaia, A., ... Hancock, R. E. W. (2010). Curating the innate immunity interactome. BMC Systems Biology, 4, [117]. https://doi.org/10.1186/1752-0509-4-117
Lynn, David J. ; Chan, Calvin ; Naseer, Misbah ; Yau, Melissa ; Lo, Raymond ; Sribnaia, Anastasia ; Ring, Giselle ; Que, Jaimmie ; Wee, Kathleen ; Winsor, Geoffrey L. ; Laird, Matthew R. ; Breuer, Karin ; Foroushani, Amir K. ; Brinkman, Fiona S L ; Hancock, Robert E W. / Curating the innate immunity interactome. In: BMC Systems Biology. 2010 ; Vol. 4.
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abstract = "Background: The innate immune response is the first line of defence against invading pathogens and is regulated by complex signalling and transcriptional networks. Systems biology approaches promise to shed new light on the regulation of innate immunity through the analysis and modelling of these networks. A key initial step in this process is the contextual cataloguing of the components of this system and the molecular interactions that comprise these networks. InnateDB (http://www.innatedb.com) is a molecular interaction and pathway database developed to facilitate systems-level analyses of innate immunity.Results: Here, we describe the InnateDB curation project, which is manually annotating the human and mouse innate immunity interactome in rich contextual detail, and present our novel curation software system, which has been developed to ensure interactions are curated in a highly accurate and data-standards compliant manner. To date, over 13,000 interactions (protein, DNA and RNA) have been curated from the biomedical literature. Here, we present data, illustrating how InnateDB curation of the innate immunity interactome has greatly enhanced network and pathway annotation available for systems-level analysis and discuss the challenges that face such curation efforts. Significantly, we provide several lines of evidence that analysis of the innate immunity interactome has the potential to identify novel signalling, transcriptional and post-transcriptional regulators of innate immunity. Additionally, these analyses also provide insight into the cross-talk between innate immunity pathways and other biological processes, such as adaptive immunity, cancer and diabetes, and intriguingly, suggests links to other pathways, which as yet, have not been implicated in the innate immune response.Conclusions: In summary, curation of the InnateDB interactome provides a wealth of information to enable systems-level analysis of innate immunity.",
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Lynn, DJ, Chan, C, Naseer, M, Yau, M, Lo, R, Sribnaia, A, Ring, G, Que, J, Wee, K, Winsor, GL, Laird, MR, Breuer, K, Foroushani, AK, Brinkman, FSL & Hancock, REW 2010, 'Curating the innate immunity interactome', BMC Systems Biology, vol. 4, 117. https://doi.org/10.1186/1752-0509-4-117

Curating the innate immunity interactome. / Lynn, David J.; Chan, Calvin; Naseer, Misbah; Yau, Melissa; Lo, Raymond; Sribnaia, Anastasia; Ring, Giselle; Que, Jaimmie; Wee, Kathleen; Winsor, Geoffrey L.; Laird, Matthew R.; Breuer, Karin; Foroushani, Amir K.; Brinkman, Fiona S L; Hancock, Robert E W.

In: BMC Systems Biology, Vol. 4, 117, 20.08.2010.

Research output: Contribution to journalArticle

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T1 - Curating the innate immunity interactome

AU - Lynn, David J.

AU - Chan, Calvin

AU - Naseer, Misbah

AU - Yau, Melissa

AU - Lo, Raymond

AU - Sribnaia, Anastasia

AU - Ring, Giselle

AU - Que, Jaimmie

AU - Wee, Kathleen

AU - Winsor, Geoffrey L.

AU - Laird, Matthew R.

AU - Breuer, Karin

AU - Foroushani, Amir K.

AU - Brinkman, Fiona S L

AU - Hancock, Robert E W

PY - 2010/8/20

Y1 - 2010/8/20

N2 - Background: The innate immune response is the first line of defence against invading pathogens and is regulated by complex signalling and transcriptional networks. Systems biology approaches promise to shed new light on the regulation of innate immunity through the analysis and modelling of these networks. A key initial step in this process is the contextual cataloguing of the components of this system and the molecular interactions that comprise these networks. InnateDB (http://www.innatedb.com) is a molecular interaction and pathway database developed to facilitate systems-level analyses of innate immunity.Results: Here, we describe the InnateDB curation project, which is manually annotating the human and mouse innate immunity interactome in rich contextual detail, and present our novel curation software system, which has been developed to ensure interactions are curated in a highly accurate and data-standards compliant manner. To date, over 13,000 interactions (protein, DNA and RNA) have been curated from the biomedical literature. Here, we present data, illustrating how InnateDB curation of the innate immunity interactome has greatly enhanced network and pathway annotation available for systems-level analysis and discuss the challenges that face such curation efforts. Significantly, we provide several lines of evidence that analysis of the innate immunity interactome has the potential to identify novel signalling, transcriptional and post-transcriptional regulators of innate immunity. Additionally, these analyses also provide insight into the cross-talk between innate immunity pathways and other biological processes, such as adaptive immunity, cancer and diabetes, and intriguingly, suggests links to other pathways, which as yet, have not been implicated in the innate immune response.Conclusions: In summary, curation of the InnateDB interactome provides a wealth of information to enable systems-level analysis of innate immunity.

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Lynn DJ, Chan C, Naseer M, Yau M, Lo R, Sribnaia A et al. Curating the innate immunity interactome. BMC Systems Biology. 2010 Aug 20;4. 117. https://doi.org/10.1186/1752-0509-4-117