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Background  The advent of high-throughput technologies to profile human tumors has generated unprecedented insight into our molecular understanding of cancer. However, analysis of such high dimensional data is challenging and requires significant expertise which is not routinely available to many cancer researchers.    Results  To overcome this limitation, we developed a freely accessible and user friendly Program to Identify Molecular Signatures (PIMS). Importantly, such signatures allow important insight into cancer biology, as well as provide clinical tools to identify potential biomarkers that might provide means to accurately stratify patients into different risk or treatment groups. We evaluated the performance of PIMS by identifying and testing predictive and prognostic gene signatures for breast cancer, using multiple breast tumor microarray cohorts representing hundreds of patients. Importantly, PIMS identified signatures classified patients into high and low risk groups with at least similar performance to other commonly used gene signature selection techniques.    Conclusions  Our program is contained entirely within a Microsoft Excel file and therefore requires no installation of any additional programs or training. Hence, PIMS provides an accessible tool for cancer researchers to identify predictive and prognostic gene signatures to advance their research.    Electronic supplementary material  The online version of this article (doi:10.1186/1756-0500-7-546) contains supplementary material, which is available to authorized users.

A program to identify prognostic and predictive gene signatures