title: Survival Online: a web-based service for the analysis of correlations between gene expression and clinical and follow-up data.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: University of Genoa, Department of Communication, Computer and System Sciences, Viale Causa 13, Genoa, Italy. luca.corradi@unige.it
authors.forename: Luca
authors.initials: L
authors.lastname: Corradi
authors.forename: Valentina
authors.initials: V
authors.lastname: Mirisola
authors.forename: Ivan
authors.initials: I
authors.lastname: Porro
authors.forename: Livia
authors.initials: L
authors.lastname: Torterolo
authors.forename: Marco
authors.initials: M
authors.lastname: Fato
authors.forename: Paolo
authors.initials: P
authors.lastname: Romano
authors.forename: Ulrich
authors.initials: U
authors.lastname: Pfeffer
mesh_terms: D001943:Breast Neoplasms / Q000175:diagnosis / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D005260:Female; D005500:Follow-Up Studies; D015870:Gene Expression; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D020407:Internet; D012984:Software; D014584:User-Computer Interface