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. 2014 Dec 17:14:970.
doi: 10.1186/1471-2407-14-970.

PROGgeneV2: enhancements on the existing database

Chirayu Pankaj Goswami  1 , Harikrishna Nakshatri
Affiliations

PROGgeneV2: enhancements on the existing database

Chirayu Pankaj Goswami et al. BMC Cancer. .

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.

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Figures

Figure 1
Figure 1
Comparison of number of datasets available in PROGgeneV1 and V2.
Figure 2
Figure 2
Number of samples in datasets that are included in PROGgeneV2.
Figure 3
Figure 3
A line diagram depicting workflow of PROGgeneV2 program.
See this image and copyright information in PMC

References

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

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