Abstract
Abstract Cancer is a genetic disease whose biology is driven by mutated and abnormally expressed genes. In the past ∼15 years, the identification of diagnostic and prognostic biomarkers from genomic data has increased our understanding of cancer biology and has led to advances in the personalized treatment of many cancers. Despite these advances, however, there are no clinically approved biomarkers for the treatment of bladder cancer, which is the fourth most common cancer in males in the United States and one of the most expensive cancers to treat. Although gene expression profiles of bladder cancer patients are publicly available, their analysis is time-consuming and requires computational resources and bioinformatics expertise often not available to biologists or clinician-researchers. Here we describe BC-BET, an online Bladder Cancer Biomarker Evaluation Tool for evaluating candidate diagnostic and prognostic biomarkers in bladder cancer. The BC-BET database contains gene expression data collected from 11 publicly available patient cohorts (N = 1041). For a chosen gene, BC-BET evaluates whether the gene is differentially expressed (P < 0.05) between normal cells and tumors, between low-grade (LG) and high-grade (HG) tumors, and between non-muscle invasive (NMI) and muscle invasive (MI) tumors. Survival analysis is carried out to evaluate whether gene expression is significantly associated with survival in all patients, or in clinically important subsets of patients with NMI, LG tumors, or in patients with MI, HG tumors. Results are summarized graphically and can be downloaded in an Excel spreadsheet. A user can also look at the relative expression of a gene or the correlation between the expression of two genes across 40 bladder cancer cell lines. This tool is freely available to the cancer research community and will be updated as additional bladder cancer biomarker data becomes available. BC-BET is available from http://bioinformatics.easternct.edu. Citation Format: Garrett Dancik. BC-BET: an online bladder cancer biomarker evaluation tool. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2168. doi:10.1158/1538-7445.AM2015-2168
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