SurvExpress: An Online Biomarker Validation Tool and Database for Cancer Gene Expression Data Using Survival Analysis

Raul Aguirre-Gamboa, Hugo Gomez-Rueda, Emmanuel Martínez-Ledesma, Antonio Martínez-Torteya, Rafael Chacolla-Huaringa, Alberto Rodriguez-Barrientos, José G. Tamez-Peña, Victor Treviño

Resultado de la investigación

290 Citas (Scopus)

Resumen

Validation of multi-gene biomarkers for clinical outcomes is one of the most important issues for cancer prognosis. An important source of information for virtual validation is the high number of available cancer datasets. Nevertheless, assessing the prognostic performance of a gene expression signature along datasets is a difficult task for Biologists and Physicians and also time-consuming for Statisticians and Bioinformaticians. Therefore, to facilitate performance comparisons and validations of survival biomarkers for cancer outcomes, we developed SurvExpress, a cancer-wide gene expression database with clinical outcomes and a web-based tool that provides survival analysis and risk assessment of cancer datasets. The main input of SurvExpress is only the biomarker gene list. We generated a cancer database collecting more than 20,000 samples and 130 datasets with censored clinical information covering tumors over 20 tissues. We implemented a web interface to perform biomarker validation and comparisons in this database, where a multivariate survival analysis can be accomplished in about one minute. We show the utility and simplicity of SurvExpress in two biomarker applications for breast and lung cancer. Compared to other tools, SurvExpress is the largest, most versatile, and quickest free tool available. SurvExpress web can be accessed in http://bioinformatica.mty.itesm.mx/SurvExpress (a tutorial is included). The website was implemented in JSP, JavaScript, MySQL, and R. © 2013 Aguirre-Gamboa et al.
Idioma originalEnglish
PublicaciónPLoS One
DOI
EstadoPublished - 16 sep 2013
Publicado de forma externa

Huella dactilar

Neoplasm Genes
Biomarkers
Survival Analysis
Gene expression
biomarkers
Databases
Gene Expression
gene expression
neoplasms
Neoplasms
Genes
Tumor Biomarkers
Risk assessment
Websites
Tumors
Transcriptome
Tissue
Lung Neoplasms
Multivariate Analysis
lung neoplasms

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Citar esto

Aguirre-Gamboa, R., Gomez-Rueda, H., Martínez-Ledesma, E., Martínez-Torteya, A., Chacolla-Huaringa, R., Rodriguez-Barrientos, A., ... Treviño, V. (2013). SurvExpress: An Online Biomarker Validation Tool and Database for Cancer Gene Expression Data Using Survival Analysis. PLoS One. https://doi.org/10.1371/journal.pone.0074250
Aguirre-Gamboa, Raul ; Gomez-Rueda, Hugo ; Martínez-Ledesma, Emmanuel ; Martínez-Torteya, Antonio ; Chacolla-Huaringa, Rafael ; Rodriguez-Barrientos, Alberto ; Tamez-Peña, José G. ; Treviño, Victor. / SurvExpress: An Online Biomarker Validation Tool and Database for Cancer Gene Expression Data Using Survival Analysis. En: PLoS One. 2013.
@article{024a31485a944666921be1ada8d72f4c,
title = "SurvExpress: An Online Biomarker Validation Tool and Database for Cancer Gene Expression Data Using Survival Analysis",
abstract = "Validation of multi-gene biomarkers for clinical outcomes is one of the most important issues for cancer prognosis. An important source of information for virtual validation is the high number of available cancer datasets. Nevertheless, assessing the prognostic performance of a gene expression signature along datasets is a difficult task for Biologists and Physicians and also time-consuming for Statisticians and Bioinformaticians. Therefore, to facilitate performance comparisons and validations of survival biomarkers for cancer outcomes, we developed SurvExpress, a cancer-wide gene expression database with clinical outcomes and a web-based tool that provides survival analysis and risk assessment of cancer datasets. The main input of SurvExpress is only the biomarker gene list. We generated a cancer database collecting more than 20,000 samples and 130 datasets with censored clinical information covering tumors over 20 tissues. We implemented a web interface to perform biomarker validation and comparisons in this database, where a multivariate survival analysis can be accomplished in about one minute. We show the utility and simplicity of SurvExpress in two biomarker applications for breast and lung cancer. Compared to other tools, SurvExpress is the largest, most versatile, and quickest free tool available. SurvExpress web can be accessed in http://bioinformatica.mty.itesm.mx/SurvExpress (a tutorial is included). The website was implemented in JSP, JavaScript, MySQL, and R. {\circledC} 2013 Aguirre-Gamboa et al.",
author = "Raul Aguirre-Gamboa and Hugo Gomez-Rueda and Emmanuel Mart{\'i}nez-Ledesma and Antonio Mart{\'i}nez-Torteya and Rafael Chacolla-Huaringa and Alberto Rodriguez-Barrientos and Tamez-Pe{\~n}a, {Jos{\'e} G.} and Victor Trevi{\~n}o",
year = "2013",
month = "9",
day = "16",
doi = "10.1371/journal.pone.0074250",
language = "English",
journal = "PLoS One",
issn = "1932-6203",
publisher = "Public Library of Science",

}

Aguirre-Gamboa, R, Gomez-Rueda, H, Martínez-Ledesma, E, Martínez-Torteya, A, Chacolla-Huaringa, R, Rodriguez-Barrientos, A, Tamez-Peña, JG & Treviño, V 2013, 'SurvExpress: An Online Biomarker Validation Tool and Database for Cancer Gene Expression Data Using Survival Analysis', PLoS One. https://doi.org/10.1371/journal.pone.0074250

SurvExpress: An Online Biomarker Validation Tool and Database for Cancer Gene Expression Data Using Survival Analysis. / Aguirre-Gamboa, Raul; Gomez-Rueda, Hugo; Martínez-Ledesma, Emmanuel; Martínez-Torteya, Antonio; Chacolla-Huaringa, Rafael; Rodriguez-Barrientos, Alberto; Tamez-Peña, José G.; Treviño, Victor.

En: PLoS One, 16.09.2013.

Resultado de la investigación

TY - JOUR

T1 - SurvExpress: An Online Biomarker Validation Tool and Database for Cancer Gene Expression Data Using Survival Analysis

AU - Aguirre-Gamboa, Raul

AU - Gomez-Rueda, Hugo

AU - Martínez-Ledesma, Emmanuel

AU - Martínez-Torteya, Antonio

AU - Chacolla-Huaringa, Rafael

AU - Rodriguez-Barrientos, Alberto

AU - Tamez-Peña, José G.

AU - Treviño, Victor

PY - 2013/9/16

Y1 - 2013/9/16

N2 - Validation of multi-gene biomarkers for clinical outcomes is one of the most important issues for cancer prognosis. An important source of information for virtual validation is the high number of available cancer datasets. Nevertheless, assessing the prognostic performance of a gene expression signature along datasets is a difficult task for Biologists and Physicians and also time-consuming for Statisticians and Bioinformaticians. Therefore, to facilitate performance comparisons and validations of survival biomarkers for cancer outcomes, we developed SurvExpress, a cancer-wide gene expression database with clinical outcomes and a web-based tool that provides survival analysis and risk assessment of cancer datasets. The main input of SurvExpress is only the biomarker gene list. We generated a cancer database collecting more than 20,000 samples and 130 datasets with censored clinical information covering tumors over 20 tissues. We implemented a web interface to perform biomarker validation and comparisons in this database, where a multivariate survival analysis can be accomplished in about one minute. We show the utility and simplicity of SurvExpress in two biomarker applications for breast and lung cancer. Compared to other tools, SurvExpress is the largest, most versatile, and quickest free tool available. SurvExpress web can be accessed in http://bioinformatica.mty.itesm.mx/SurvExpress (a tutorial is included). The website was implemented in JSP, JavaScript, MySQL, and R. © 2013 Aguirre-Gamboa et al.

AB - Validation of multi-gene biomarkers for clinical outcomes is one of the most important issues for cancer prognosis. An important source of information for virtual validation is the high number of available cancer datasets. Nevertheless, assessing the prognostic performance of a gene expression signature along datasets is a difficult task for Biologists and Physicians and also time-consuming for Statisticians and Bioinformaticians. Therefore, to facilitate performance comparisons and validations of survival biomarkers for cancer outcomes, we developed SurvExpress, a cancer-wide gene expression database with clinical outcomes and a web-based tool that provides survival analysis and risk assessment of cancer datasets. The main input of SurvExpress is only the biomarker gene list. We generated a cancer database collecting more than 20,000 samples and 130 datasets with censored clinical information covering tumors over 20 tissues. We implemented a web interface to perform biomarker validation and comparisons in this database, where a multivariate survival analysis can be accomplished in about one minute. We show the utility and simplicity of SurvExpress in two biomarker applications for breast and lung cancer. Compared to other tools, SurvExpress is the largest, most versatile, and quickest free tool available. SurvExpress web can be accessed in http://bioinformatica.mty.itesm.mx/SurvExpress (a tutorial is included). The website was implemented in JSP, JavaScript, MySQL, and R. © 2013 Aguirre-Gamboa et al.

U2 - 10.1371/journal.pone.0074250

DO - 10.1371/journal.pone.0074250

M3 - Article

JO - PLoS One

JF - PLoS One

SN - 1932-6203

ER -