AI Article Synopsis
- The article discusses a new method for analyzing complex microarray gene expression data in relation to clinical and pathological data, with a focus on validating biomarkers and multi-gene classifiers.
- A web-based system called "Survival Online" was developed to allow users to easily analyze Affymetrix GeneChip microarrays, enabling correlation of gene expression values with clinical data through regression and survival analysis.
- The system is user-friendly for researchers without advanced computational skills and is designed to handle multiple datasets efficiently using high-performance computing resources.
Article Abstract
Background: 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.
Results: 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.
Conclusion: 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.
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|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2762059 | PMC |
| http://dx.doi.org/10.1186/1471-2105-10-S12-S10 | DOI Listing |
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