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Chang AB, Marsh RL, Upham JW, Hoffman LR, Smith-Vaughan H, Holt D, Toombs M, Byrnes C, Yerkovich ST, Torzillo PJ, O'Grady KAF, Grimwood K. Toward making inroads in reducing the disparity of lung health in Australian indigenous and new zealand māori children. Front Pediatr 2015; 3:9. [PMID: 25741502 PMCID: PMC4327127 DOI: 10.3389/fped.2015.00009] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 01/26/2015] [Indexed: 01/01/2023] Open
Affiliation(s)
- Anne B Chang
- Child Health Division, Menzies School of Health Research, Charles Darwin University , Darwin, NT , Australia ; Queensland Children's Medical Research Institute, Queensland University of Technology , Brisbane, QLD , Australia
| | - Robyn L Marsh
- Child Health Division, Menzies School of Health Research, Charles Darwin University , Darwin, NT , Australia
| | - John W Upham
- Department of Respiratory Medicine, Princess Alexandra Hospital , Brisbane, QLD , Australia ; School of Medicine, The University of Queensland , Brisbane, QLD , Australia
| | - Lucas R Hoffman
- Department of Pediatrics, University of Washington , Seattle, WA , USA ; Department of Microbiology, University of Washington , Seattle, WA , USA
| | - Heidi Smith-Vaughan
- Child Health Division, Menzies School of Health Research, Charles Darwin University , Darwin, NT , Australia
| | - Deborah Holt
- Child Health Division, Menzies School of Health Research, Charles Darwin University , Darwin, NT , Australia
| | - Maree Toombs
- Child Health Division, Menzies School of Health Research, Charles Darwin University , Darwin, NT , Australia ; Indigenous Health, Toowoomba Rural Clinical School, The University of Queensland , Toowoomba, QLD , Australia
| | - Catherine Byrnes
- Paediatric Department, University of Auckland & Starship Children's Hospital , Auckland , New Zealand
| | - Stephanie T Yerkovich
- Child Health Division, Menzies School of Health Research, Charles Darwin University , Darwin, NT , Australia ; School of Medicine, The University of Queensland , Brisbane, QLD , Australia ; Queensland Lung Transplant Service, The Prince Charles Hospital , Chermside, QLD , Australia
| | - Paul J Torzillo
- Nganampa Health Council, Alice Springs and Royal Prince Alfred Hospital, The University of Sydney , Sydney, NSW , Australia
| | - Kerry-Ann F O'Grady
- Queensland Children's Medical Research Institute, Queensland University of Technology , Brisbane, QLD , Australia
| | - Keith Grimwood
- Gold Coast University Hospital, Griffith University , Gold Coast, QLD , Australia
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Hur J, Ozgür A, Xiang Z, He Y. Identification of fever and vaccine-associated gene interaction networks using ontology-based literature mining. J Biomed Semantics 2012; 3:18. [PMID: 23256563 PMCID: PMC3599673 DOI: 10.1186/2041-1480-3-18] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 11/23/2012] [Indexed: 12/03/2022] Open
Abstract
Background Fever is one of the most common adverse events of vaccines. The detailed mechanisms of fever and vaccine-associated gene interaction networks are not fully understood. In the present study, we employed a genome-wide, Centrality and Ontology-based Network Discovery using Literature data (CONDL) approach to analyse the genes and gene interaction networks associated with fever or vaccine-related fever responses. Results Over 170,000 fever-related articles from PubMed abstracts and titles were retrieved and analysed at the sentence level using natural language processing techniques to identify genes and vaccines (including 186 Vaccine Ontology terms) as well as their interactions. This resulted in a generic fever network consisting of 403 genes and 577 gene interactions. A vaccine-specific fever sub-network consisting of 29 genes and 28 gene interactions was extracted from articles that are related to both fever and vaccines. In addition, gene-vaccine interactions were identified. Vaccines (including 4 specific vaccine names) were found to directly interact with 26 genes. Gene set enrichment analysis was performed using the genes in the generated interaction networks. Moreover, the genes in these networks were prioritized using network centrality metrics. Making scientific discoveries and generating new hypotheses were possible by using network centrality and gene set enrichment analyses. For example, our study found that the genes in the generic fever network were more enriched in cell death and responses to wounding, and the vaccine sub-network had more gene enrichment in leukocyte activation and phosphorylation regulation. The most central genes in the vaccine-specific fever network are predicted to be highly relevant to vaccine-induced fever, whereas genes that are central only in the generic fever network are likely to be highly relevant to generic fever responses. Interestingly, no Toll-like receptors (TLRs) were found in the gene-vaccine interaction network. Since multiple TLRs were found in the generic fever network, it is reasonable to hypothesize that vaccine-TLR interactions may play an important role in inducing fever response, which deserves a further investigation. Conclusions This study demonstrated that ontology-based literature mining is a powerful method for analyzing gene interaction networks and generating new scientific hypotheses.
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Affiliation(s)
- Junguk Hur
- Unit for Laboratory Animal Medicine, University of Michigan, 48109, Ann Arbor, MI, USA.
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