Classification of Dengue Fever Patients Based on Gene Expression Data Using Support Vector Machines
| Autor(a) principal: | |
|---|---|
| Data de Publicação: | 2010 |
| Outros Autores: | , , , , , |
| Tipo de documento: | Artigo |
| Idioma: | eng |
| Título da fonte: | Repositório Institucional da FIOCRUZ (ARCA) |
| DOI: | 10.1371/journal.pone.0011267 |
| Texto Completo: | https://www.arca.fiocruz.br/handle/icict/5616 |
Resumo: | Fundação Oswaldo Cruz. Centro de Pesquisas Aggeu Magalhaes. Departamento de Virologia e Terapia Experimental. Recife, PE, Brazil. |
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Gomes, Ana Lisa V.Wee, Lawrence J. K.Khan, Asif M.Gil, Laura H. V. G.Marques Júnior, Ernesto Torres de AzevedoSilva, Carlos Eduardo CalzavaraTan, Tin Wee2012-09-28T17:13:01Z2012-09-28T17:13:01Z2010GOMES, Ana Lisa V. et al. Classification of Dengue Fever Patients Based on Gene Expression Data Using Support Vector Machines. PLoS ONE, v. 5, n. 6, p. 1-7, 2010.19326203https://www.arca.fiocruz.br/handle/icict/561610.1371/journal.pone.0011267engPublic Library of ScienceGomes ALV, Wee LJK, Khan AM, Gil LHVG, Marques ETA Jr, et al. (2010) Classification of Dengue Fever Patients Based on Gene Expression Data Using Support Vector Machines. PLoS ONE 5(6): e11267.DengueClassification of Dengue Fever Patients Based on Gene Expression Data Using Support Vector Machinesinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleFundação Oswaldo Cruz. Centro de Pesquisas Aggeu Magalhaes. Departamento de Virologia e Terapia Experimental. Recife, PE, Brazil.National University of Singapore. Yong Loo Lin School of Medicine. Department of Biochemistry. Singapore, Singapore.National University of Singapore. Yong Loo Lin School of Medicine. Department of Biochemistry. Singapore, Singapore.Fundação Oswaldo Cruz. Centro de Pesquisas Aggeu Magalhaes. Departamento de Virologia e Terapia Experimental. Recife, PE, Brazil.Fundação Oswaldo Cruz. Centro de Pesquisas Aggeu Magalhaes. Departamento de Virologia e Terapia Experimental. Recife, PE, Brazil/University of Pittsburgh. Center for Vaccine Research. Department of Infectious Diseases and Microbiology. Pittsburgh, Pennsylvania, United States of America.Fundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Departamento de Imunologia Celular e Molecular. Belo Horizonte, MG, Brazil.National University of Singapore. Yong Loo Lin School of Medicine. Department of Biochemistry. Singapore, Singapore.Background: Symptomatic infection by dengue virus (DENV) can range from dengue fever (DF) to dengue haemorrhagic fever (DHF), however, the determinants of DF or DHF progression are not completely understood. It is hypothesised that host innate immune response factors are involved in modulating the disease outcome and the expression levels of genes involved in this response could be used as early prognostic markers for disease severity. Methodology/Principal Findings: mRNA expression levels of genes involved in DENV innate immune responses were measured using quantitative real time PCR (qPCR). Here, we present a novel application of the support vector machines (SVM) algorithm to analyze the expression pattern of 12 genes in peripheral blood mononuclear cells (PBMCs) of 28 dengue patients (13 DHF and 15 DF) during acute viral infection. The SVM model was trained using gene expression data of these genes and achieved the highest accuracy of ,85% with leave-one-out cross-validation. Through selective removal of gene expression data from the SVM model, we have identified seven genes (MYD88, TLR7, TLR3, MDA5, IRF3, IFN-a and CLEC5A) that may be central in differentiating DF patients from DHF, with MYD88 and TLR7 observed to be the most important. Though the individual removal of expression data of five other genes had no impact on the overall accuracy, a significant combined role was observed when the SVM model of the two main genes (MYD88 and TLR7) was re-trained to include the five genes, increasing the overall accuracy to ,96%. Conclusions/Significance: Here, we present a novel use of the SVM algorithm to classify DF and DHF patients, as well as to elucidate the significance of the various genes involved. It was observed that seven genes are critical in classifying DF and DHF patients: TLR3, MDA5, IRF3, IFN-a, CLEC5A, and the two most important MYD88 and TLR7. 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| dc.title.pt_BR.fl_str_mv |
Classification of Dengue Fever Patients Based on Gene Expression Data Using Support Vector Machines |
| title |
Classification of Dengue Fever Patients Based on Gene Expression Data Using Support Vector Machines |
| spellingShingle |
Classification of Dengue Fever Patients Based on Gene Expression Data Using Support Vector Machines Gomes, Ana Lisa V. Dengue |
| title_short |
Classification of Dengue Fever Patients Based on Gene Expression Data Using Support Vector Machines |
| title_full |
Classification of Dengue Fever Patients Based on Gene Expression Data Using Support Vector Machines |
| title_fullStr |
Classification of Dengue Fever Patients Based on Gene Expression Data Using Support Vector Machines |
| title_full_unstemmed |
Classification of Dengue Fever Patients Based on Gene Expression Data Using Support Vector Machines |
| title_sort |
Classification of Dengue Fever Patients Based on Gene Expression Data Using Support Vector Machines |
| author |
Gomes, Ana Lisa V. |
| author_facet |
Gomes, Ana Lisa V. Wee, Lawrence J. K. Khan, Asif M. Gil, Laura H. V. G. Marques Júnior, Ernesto Torres de Azevedo Silva, Carlos Eduardo Calzavara Tan, Tin Wee |
| author_role |
author |
| author2 |
Wee, Lawrence J. K. Khan, Asif M. Gil, Laura H. V. G. Marques Júnior, Ernesto Torres de Azevedo Silva, Carlos Eduardo Calzavara Tan, Tin Wee |
| author2_role |
author author author author author author |
| dc.contributor.author.fl_str_mv |
Gomes, Ana Lisa V. Wee, Lawrence J. K. Khan, Asif M. Gil, Laura H. V. G. Marques Júnior, Ernesto Torres de Azevedo Silva, Carlos Eduardo Calzavara Tan, Tin Wee |
| dc.subject.other.pt_BR.fl_str_mv |
Dengue |
| topic |
Dengue |
| description |
Fundação Oswaldo Cruz. Centro de Pesquisas Aggeu Magalhaes. Departamento de Virologia e Terapia Experimental. Recife, PE, Brazil. |
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2010 |
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2010 |
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2012-09-28T17:13:01Z |
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2012-09-28T17:13:01Z |
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GOMES, Ana Lisa V. et al. Classification of Dengue Fever Patients Based on Gene Expression Data Using Support Vector Machines. PLoS ONE, v. 5, n. 6, p. 1-7, 2010. |
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19326203 |
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10.1371/journal.pone.0011267 |
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GOMES, Ana Lisa V. et al. Classification of Dengue Fever Patients Based on Gene Expression Data Using Support Vector Machines. PLoS ONE, v. 5, n. 6, p. 1-7, 2010. 19326203 10.1371/journal.pone.0011267 |
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Gomes ALV, Wee LJK, Khan AM, Gil LHVG, Marques ETA Jr, et al. (2010) Classification of Dengue Fever Patients Based on Gene Expression Data Using Support Vector Machines. PLoS ONE 5(6): e11267. |
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