Gene expression and survival analysis in cancer research using online open access platforms: a comparative analysis

Sofia Ramos; Ana Sofia Fernandes; Nuno Saraiva

doi:10.19277/BBR.17.2.247

Gene expression and survival analysis in cancer research using online open access platforms: a comparative analysis

Título traduzido da contribuição: Plataformas “open access” para análise de expressão génica e sobrevida em oncologia: uma análise comparativa

Sofia Ramos, Ana Sofia Fernandes, Nuno Saraiva

Resultado de pesquisa › revisão de pares

3 Transferências (Pure)

Resumo

O desenvolvimento da genómica e transcriptómica e o potencial associado à partilha de dados relacionados com o cancro levaram a uma crescente compreensão da sua biologia e à identificação de novos biomarcadores. A análise da expressão génica do tumor e a taxa de sobrevida do doente associada, permitem explorar o impacto de um determinado gene na sobrevida do doente com cancro. Para isso, é essencial escolher plataformas simples de usar, onde seja fácil analisar, comparar e recolher informações para um determinado conjunto de genes de interesse. O objetivo deste artigo é comparar o conteúdo e utilidade de cinco plataformas on-line de acesso aberto para expressão de genes tumorais e análise da sobrevida de doentes a partir de conjuntos de dados do TCGA - cBioPortal, UCSC Xena, GEPIA, UALCAN e ONCOLNC. Exploramos as plataformas acima mencionadas do ponto de vista de um utilizador médio, avaliando a sua aplicabilidade no estudo de diferenças na expressão génica em tecidos tumorais vs tecidos normais, ou de acordo com o estádio do cancro, e o impacto desse padrão de expressão na sobrevida do doente. Embora todas as cinco plataformas sejam muito intuitivas e o acesso aos dados seja fácil, elas variam nas informações disponibilizadas, na visualização dos resultados e nos testes estatísticos realizados. Logo, a escolha de uma plataforma deve ter em consideração os objetivos do estudo. Para alguns propósitos, pode ser necessária uma combinação de plataformas. Palavras-chave: Bases de dados do TCGA; plataformas de open access; expressão génica tumoral; sobrevida do doente

Título traduzido da contribuição	Plataformas “open access” para análise de expressão génica e sobrevida em oncologia: uma análise comparativa
Idioma original	Inglês
Páginas (de-até)	222-240
Número de páginas	19
Revista	Biomedical and biopharmaceutical research : jornal de investigação biomédica e biofarmacêutica
Volume	17
Número de emissão	2
DOIs	https://doi.org/10.19277/BBR.17.2.247
Estado da publicação	Publicadas - 2020

Nota bibliográfica

Publisher Copyright:
© Universidade Lusófona 2020. All rights reserved.

Keywords

MEDICINA
BIOMEDICINA
ACESSO LIVRE
ANÁLISE DE SOBREVIVÊNCIA
EXPRESSÃO GÉNICA
NEOPLASIAS

ODS da ONU

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abstract = "The development of genomics and transcriptomics and the potential associated with sharing data related with cancer, led to a growing understanding of cancer biology and to the identification of new biomarkers. Analysis of tumor gene expression and associated patient survival rate enables the dissection of the impact of certain genes in cancer patient´s survival. For that purpose, it is essential to choose user-friendly platforms, where it is easy to analyze, compare and collect information for a certain set of genes. The goal of this article is to compare the content and utility of five open access online platforms for tumor gene expression and patient survival analysis from TCGA datasets – cBioPortal, USCS Xena, GEPIA, UALCAN and ONCOLNC. We explore these platforms from the point of view of a lay user, assessing their applicability to study differences in gene expression in tumor vs normal tissues, or according to cancer stage, and the impact of such expression patterns on patient survival. Although all five platforms are very intuitive and access to the data is easy, they vary in the information available, results visualization, and statistical tests performed. Therefore, the choice of a platform must take into account the study goals. For some purposes, a combination of platforms may be required. Keywords: TCGA datasets, open access platforms, tumor gene expression, patient survival",

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Gene expression and survival analysis in cancer research using online open access platforms: a comparative analysis

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