MethSurv: a web tool to perform multivariable survival analysis using DNA methylation data

Epigenomics. 2018 Mar;10(3):277-288. doi: 10.2217/epi-2017-0118. Epub 2017 Dec 21.

Abstract

Aim: To develop a web tool for survival analysis based on CpG methylation patterns.

Materials & methods: We utilized methylome data from 'The Cancer Genome Atlas' and used the Cox proportional-hazards model to develop an interactive web interface for survival analysis.

Results: MethSurv enables survival analysis for a CpG located in or around the proximity of a query gene. For further mining, cluster analysis for a query gene to associate methylation patterns with clinical characteristics and browsing of top biomarkers for each cancer type are provided. MethSurv includes 7358 methylomes from 25 different human cancers.

Conclusion: The MethSurv tool is a valuable platform for the researchers without programming skills to perform the initial assessment of methylation-based cancer biomarkers.

Keywords: Cox Proportional-Hazards; DNA methylation; Illumina 450 K; Kaplan–Meier; TCGA; biomarkers; cancer survival analysis; clustering; epigenetics; prognosis.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Atlases as Topic
  • Cluster Analysis
  • Computational Biology / methods*
  • CpG Islands
  • DNA Methylation*
  • DNA, Neoplasm / genetics*
  • DNA, Neoplasm / metabolism
  • Data Mining
  • Epigenesis, Genetic*
  • Genome, Human
  • Humans
  • Kaplan-Meier Estimate
  • Molecular Sequence Annotation
  • Neoplasms / diagnosis
  • Neoplasms / genetics*
  • Neoplasms / metabolism
  • Neoplasms / mortality
  • Proportional Hazards Models
  • Software*

Substances

  • DNA, Neoplasm