PROGgeneV2: Enhancements on the existing database

Chirayu Pankaj Goswami, Harikrishna Nakshatri

Research output: Contribution to journalArticle

168 Scopus citations

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.

Original languageEnglish (US)
Article number970
JournalBMC Cancer
Volume14
Issue number1
DOIs
StatePublished - Dec 17 2014

Keywords

  • Biomarker
  • Database
  • KM
  • Kaplan
  • Meier
  • Multiple cancer
  • Pan cancer
  • Prognostic
  • Survival
  • mRNA

ASJC Scopus subject areas

  • Genetics
  • Oncology
  • Cancer Research

Fingerprint Dive into the research topics of 'PROGgeneV2: Enhancements on the existing database'. Together they form a unique fingerprint.

  • Cite this