iBAG: integrative Bayesian analysis of high-dimensional multiplatform genomics data

Bioinformatics. 2013 Jan 15;29(2):149-59. doi: 10.1093/bioinformatics/bts655. Epub 2012 Nov 9.


Motivation: Analyzing data from multi-platform genomics experiments combined with patients' clinical outcomes helps us understand the complex biological processes that characterize a disease, as well as how these processes relate to the development of the disease. Current data integration approaches are limited in that they do not consider the fundamental biological relationships that exist among the data obtained from different platforms. Statistical Model: We propose an integrative Bayesian analysis of genomics data (iBAG) framework for identifying important genes/biomarkers that are associated with clinical outcome. This framework uses hierarchical modeling to combine the data obtained from multiple platforms into one model.

Results: We assess the performance of our methods using several synthetic and real examples. Simulations show our integrative methods to have higher power to detect disease-related genes than non-integrative methods. Using the Cancer Genome Atlas glioblastoma dataset, we apply the iBAG model to integrate gene expression and methylation data to study their associations with patient survival. Our proposed method discovers multiple methylation-regulated genes that are related to patient survival, most of which have important biological functions in other diseases but have not been previously studied in glioblastoma.

Availability: http://odin.mdacc.tmc.edu/∼vbaladan/.

Contact: veera@mdanderson.org

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Bayes Theorem
  • Brain Neoplasms / genetics*
  • Brain Neoplasms / metabolism
  • Brain Neoplasms / mortality*
  • DNA Methylation
  • Gene Expression Profiling
  • Genomics / methods
  • Glioblastoma / genetics*
  • Glioblastoma / metabolism
  • Glioblastoma / mortality*
  • Humans
  • Models, Statistical*