Survival Online: a web-based service for the analysis of correlations between gene expression and clinical and follow-up dataReport as inadecuate




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BMC Bioinformatics

, 10:S10

First Online: 15 October 2009

Abstract

BackgroundComplex microarray gene expression datasets can be used for many independent analyses and are particularly interesting for the validation of potential biomarkers and multi-gene classifiers. This article presents a novel method to perform correlations between microarray gene expression data and clinico-pathological data through a combination of available and newly developed processing tools.

ResultsWe developed Survival Online available at http:-ada.dist.unige.it:8080-enginframe-bioinf-bioinf.xml, a Web-based system that allows for the analysis of Affymetrix GeneChip microarrays by using a parallel version of dChip. The user is first enabled to select pre-loaded datasets or single samples thereof, as well as single genes or lists of genes. Expression values of selected genes are then correlated with sample annotation data by uni- or multi-variate Cox regression and survival analyses. The system was tested using publicly available breast cancer datasets and GO Gene Ontology derived gene lists or single genes for survival analyses.

ConclusionThe system can be used by bio-medical researchers without specific computation skills to validate potential biomarkers or multi-gene classifiers. The design of the service, the parallelization of pre-processing tasks and the implementation on an HPC High Performance Computing environment make this system a useful tool for validation on several independent datasets.

Luca Corradi, Valentina Mirisola, Ivan Porro, Livia Torterolo, Marco Fato, Paolo Romano and Ulrich Pfeffer contributed equally to this work.

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Author: Luca Corradi - Valentina Mirisola - Ivan Porro - Livia Torterolo - Marco Fato - Paolo Romano - Ulrich Pfeffer

Source: https://link.springer.com/







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