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PROGgene: gene expression based survival analysis web application for multiple cancers

Chirayu Pankaj Goswami1* and Harikrishna Nakshatri2

Author Affiliations

1 Thomas Jefferson University Hospitals, 117 S 11th Street, Suite 207, Philadelphia, PA 19107, 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 2013, 3:22  doi:10.1186/2043-9113-3-22

Published: 28 October 2013

Abstract

Background

Identification of prognostic mRNA biomarkers has been done for various cancer types. The data that are published from such studies are archived in public repositories. There are hundreds of such datasets available for multiple cancer types in public repositories. Wealth of such data can be utilized to study prognostic implications of mRNA in different cancers as well as in different populations or subtypes of same cancer.

Description

We have created a web application that can be used for studying prognostic implications of mRNA biomarkers in a variety of cancers. We have compiled data from public repositories such as GEO, EBI Array Express and The Cancer Genome Atlas for creating this tool. With 64 patient series from 18 cancer types in our database, this tool provides the most comprehensive resource available for survival analysis to date. The tool is called PROGgene and it is available at http://www.compbio.iupui.edu/proggene webcite.

Conclusions

We present this tool as a hypothesis generation tool for researchers to identify potential prognostic mRNA biomarkers to follow up with further research. For this reason, we have kept the web application very simple and straightforward. We believe this tool will be useful in accelerating biomarker discovery in cancer and quickly providing results that may indicate disease-specific prognostic value of specific biomarkers.

Keywords:
Biomarker; Multiple cancer; Survival; Pan cancer; Prognostic; mRNA; Database; Kaplan; Meier; KM