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The dChip survival analysis module for microarray data

Samir B Amin12, Parantu K Shah1, Aimin Yan1, Sophia Adamia2, Stéphane Minvielle34, Hervé Avet-Loiseau34, Nikhil C Munshi25 and Cheng Li1*

Author Affiliations

1 Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, 450 Brookline Ave, Boston, MA, 02215, USA

2 Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA

3 Hematology Department, University Hospital, Nantes, France

4 Centre de Recherche en Cancérologie, INSERM U892, Nantes, France

5 Veterans Administration Boston Healthcare System and Harvard Medical School. 1400 VFW Pkwy, West Roxbury, MA, 02132, USA

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BMC Bioinformatics 2011, 12:72  doi:10.1186/1471-2105-12-72

Published: 9 March 2011

Abstract

Background

Genome-wide expression signatures are emerging as potential marker for overall survival and disease recurrence risk as evidenced by recent commercialization of gene expression based biomarkers in breast cancer. Similar predictions have recently been carried out using genome-wide copy number alterations and microRNAs. Existing software packages for microarray data analysis provide functions to define expression-based survival gene signatures. However, there is no software that can perform survival analysis using SNP array data or draw survival curves interactively for expression-based sample clusters.

Results

We have developed the survival analysis module in the dChip software that performs survival analysis across the genome for gene expression and copy number microarray data. Built on the current dChip software's microarray analysis functions such as chromosome display and clustering, the new survival functions include interactive exploring of Kaplan-Meier (K-M) plots using expression or copy number data, computing survival p-values from the log-rank test and Cox models, and using permutation to identify significant chromosome regions associated with survival.

Conclusions

The dChip survival module provides user-friendly way to perform survival analysis and visualize the results in the context of genes and cytobands. It requires no coding expertise and only minimal learning curve for thousands of existing dChip users. The implementation in Visual C++ also enables fast computation. The software and demonstration data are freely available at http://dchip-surv.chenglilab.org webcite.