Curating the innate immunity interactome
| Autor: | Anastasia Sribnaia, Karin Breuer, Matthew R. Laird, Robert E. W. Hancock, Fiona S. L. Brinkman, David J. Lynn, Kathleen Wee, Raymond Lo, Amir Foroushani, Giselle Ring, Misbah Naseer, Geoffrey L. Winsor, Jaimmie Que, Calvin Chan, Melissa Yau |
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| Přispěvatelé: | Foundation for the National Institutes of Health and the Canadian Institutes of Health Research - Grand Challenges in Global Health Research Initiative |
| Jazyk: | angličtina |
| Rok vydání: | 2010 |
| Předmět: |
Databases
Factual Transcription Genetic First line Systems biology Innate immunity analysis Computational biology Biology Bioinformatics Interactome 03 medical and health sciences Mice 0302 clinical medicine Structural Biology Immunity Modelling and Simulation Curation software system Animals Humans lcsh:QH301-705.5 Molecular Biology 030304 developmental biology 0303 health sciences Molecular interactions Innate immune system Applied Mathematics Systems Biology Transcriptional Networks InnateDB Proteins Reproducibility of Results Molecular Sequence Annotation biochemical phenomena metabolism and nutrition Acquired immune system Immunity Innate 3. Good health Computer Science Applications MicroRNAs lcsh:Biology (General) Organ Specificity 030220 oncology & carcinogenesis Modeling and Simulation Periodicals as Topic Software Research Article |
| Zdroj: | BMC Systems Biology BMC Systems Biology, Vol 4, Iss 1, p 117 (2010) |
| Popis: | peer-reviewed 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. Genome BC - Pathogenomics of Innate Immunity (PI2) project; Foundation for the National Institutes of Health and the Canadian Institutes of Health Research - Grand Challenges in Global Health Research Initiative (Grand Challenges ID: 419); Teagasc; DJL was funded in part during this project by a postdoctoral trainee award from the Michael Smith Foundation for Health Research (MSFHR); FSLB is a Canadian Institutes of Health Research (CIHR) New Investigator and a MSFHR Senior Scholar; REWH holds a Canada Research Chair (CRC) |
| Databáze: | OpenAIRE |
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