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Integrative Bayesian Analysis of High-Dimensional Multi-Platform Genomics Data
Bioinformatics (2012)
  • Wenting Wang, The University of Texas MD Anderson Cancer Center
  • Veerabhadran Baladandayuthapani, The University of Texas MD Anderson Cancer Center
  • Jeffrey S. Morris
  • Bradley M Broom, The University of Texas MD Anderson Cancer Center
  • Ganiraju C Manyam, The University of Texas MD Anderson Cancer Center
  • Kim-Anh Do, The University of Texas MD Anderson Cancer Center
Abstract

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 integration approaches that treat the data are limited in that they do not consider the fundamental biological relationships that exist among the data from 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 a hierarchical modeling technique 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 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/

Keywords
  • Integrative analysis,
  • genomics,
  • proteomics,
  • copy number,
  • biomarkers,
  • personalized therapy,
  • Bayesian methods
Publication Date
2012
Citation Information
Wenting Wang, Veerabhadran Baladandayuthapani, Jeffrey S. Morris, Bradley M Broom, et al.. "Integrative Bayesian Analysis of High-Dimensional Multi-Platform Genomics Data" Bioinformatics (2012)
Available at: http://works.bepress.com/jeffrey_s_morris/49/