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.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Corradi L,Mirisola V,Porro I,Torterolo L,Fato M,Romano P,Pfeffer Udoi
10.1186/1471-2105-10-S12-S10subject
Has Abstractpub_date
2009-10-15 00:00:00pages
S10issn
1471-2105pii
1471-2105-10-S12-S10journal_volume
10 Suppl 12pub_type
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