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BMC Cancer

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Open Access 01-12-2014 | Software

PROGgeneV2: enhancements on the existing database

Authors: Chirayu Pankaj Goswami, Harikrishna Nakshatri

Published in: BMC Cancer | Issue 1/2014

Abstract

Background

We recently published PROGgene, a tool that can be used to study prognostic implications of genes in various cancers. The first version of the tool had several areas for improvement. In this paper we present some major enhancements we have made on the existing tool in the new version, PROGgeneV2.

Results

In PROGgeneV2, we have made several modifications to enhance survival analysis capability of the tool. First, we have increased the repository of public studies catalogued in our tool by almost two folds. We have also added additional functionalities to perform survival analysis in a variety of new ways. Survival analysis can now be performed on a) single genes b) multiple genes as a signature, c) ratio of expression of two genes, and d) curated/published gene signatures in new version. Users can now also adjust the survival analysis models for available covariates. Users can study prognostic implications of entire gene signatures in different cancer types, which are searchable by keywords. Also, unique to our tool, in the new version, users will be able to upload and use their own datasets to perform survival analysis on genes of interest.

Conclusions

We believe, like its predecessor, PROGGeneV2 will continue to be useful for the scientific community for formulating research hypotheses and designing mechanistic studies. With added datasets PROGgeneV2 is the most comprehensive survival analysis tool available. PROGgeneV2 is available at http://www.compbio.iupui.edu/proggene.

Available only for authorised users

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The pre-publication history for this paper can be accessed here:http://www.biomedcentral.com/1471-2407/14/970/prepub

Title: PROGgeneV2: enhancements on the existing database
Authors: Chirayu Pankaj Goswami
Harikrishna Nakshatri
Publication date: 01-12-2014
Publisher: BioMed Central
Published in: BMC Cancer / Issue 1/2014
Electronic ISSN: 1471-2407
DOI: https://doi.org/10.1186/1471-2407-14-970

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