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

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Author(s): Goswami Chirayu Pankaj | Nakshatri Harikrishna

Journal: Journal of Clinical Bioinformatics
ISSN 2043-9113

Volume: 2;
Issue: 1;
Start page: 23;
Date: 2012;
Original page

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

ABSTRACT
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. 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.
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