University of Genoa, Department of Communication, Computer and System Sciences, Viale Causa 13, Genoa, Italy.
BMC Bioinformatics. 2009 Oct 15;10 Suppl 12(Suppl 12):S10. doi: 10.1186/1471-2105-10-S12-S10.
Complex 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.
We 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.
The 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.
复杂的微阵列基因表达数据集可用于许多独立的分析，对于验证潜在的生物标志物和多基因分类器尤其有趣。本文提出了一种新的方法，通过组合现有的和新开发的处理工具，对微阵列基因表达数据和临床病理数据进行相关性分析。
我们开发了 Survival Online（可在 http://ada.dist.unige.it:8080/enginframe/bioinf/bioinf.xml 上获得），这是一个基于 Web 的系统，允许使用 dChip 的并行版本来分析 Affymetrix GeneChip 微阵列。用户首先可以选择预加载的数据集或其中的单个样本，以及单个基因或基因列表。然后，通过单变量或多变量 Cox 回归和生存分析，将选定基因的表达值与样本注释数据相关联。该系统使用公开的乳腺癌数据集以及用于生存分析的 GO（基因本体论）衍生基因列表或单个基因进行了测试。
该系统可供没有特定计算技能的生物医学研究人员使用，用于验证潜在的生物标志物或多基因分类器。该服务的设计、预处理任务的并行化以及在高性能计算（HPC）环境中的实现，使该系统成为在多个独立数据集上进行验证的有用工具。
