Open AccessGene expression and survival analysis in cancer research using online open access platforms: a comparative analysis
Author(s) -
Sofı́a Ramos,
Ana Sofia Fernandes,
Nuno Saraiva
Publication year - 2020
Publication title -
jornal de investigação biomédica e biofarmacêutica/jornal de investigação biomédica e biofarmacêutica
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.129
H-Index - 1
eISSN - 2182-2379
pISSN - 2182-2360
DOI - 10.19277/bbr.17.2.247
Subject(s) - identification (biology) , computer science , genomics , cancer , data science , transcriptome , computational biology , gene expression profiling , gene , gene expression , bioinformatics , biology , genome , genetics , botany
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.