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PROGmiR: a tool for identifying prognostic miRNA biomarkers in multiple cancers using publicly available data

Chirayu Pankaj Goswami1* and Harikrishna Nakshatri2

Author Affiliations

1 Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 410 W 10th Street, Indianapolis, IN, 46202, USA

2 Departments of Surgery, Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA

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Journal of Clinical Bioinformatics 2012, 2:23  doi:10.1186/2043-9113-2-23

Published: 28 December 2012

Abstract

Background

Identification of prognostic biomarkers is hallmark of cancer genomics. Since miRNAs regulate expression of multiple genes, they act as potent biomarkers in several cancers. Identification of miRNAs that are prognostically important has been done sporadically, but no resource is available till date that allows users to study prognostics of miRNAs of interest, utilizing the wealth of available data, in major cancer types.

Description

In this paper, we present a web based tool that allows users to study prognostic properties of miRNAs in several cancer types, using publicly available data. We have compiled data from Gene Expression Omnibus (GEO), and recently developed “The Cancer Genome Atlas (TCGA)”, to create this tool. The tool is called “PROGmiR” and it is available at http://www.compbio.iupui.edu/progmir webcite. Currently, our tool can be used to study overall survival implications for approximately 1050 human miRNAs in 16 major cancer types.

Conclusions

We believe this resource, as a hypothesis generation tool, will be helpful for researchers to link miRNA expression with cancer outcome and to design mechanistic studies. We studied performance of our tool using identified miRNA biomarkers from published studies. The prognostic plots created using our tool for specific miRNAs in specific cancer types corroborated with the findings in the studies.

Keywords:
miRNA; Prognostics; Cancer; Pan-cancer; Database; Signature; Biomaker