Integration of Gene Expression Data and Methylation Reveals Genetic Networks for Glioblastoma

Abstract: Motivation: The consistent amount of different types of omics data requires novel methods of analysis and data integration. In this work we describe Regression2Net, a computational approach to analyse gene expression and methylation profiles via regression analysis and network-based techniques. Results: We identified 284 and 447 unique candidate genes potentially associated to the Glioblastoma pathology from two networks inferred from mixed genetic datasets. In-depth biological analysis of these networks reveals genes that are related to energy metabolism, cell cycle control (AATF), immune system response and several types of cancer. Importantly, we observed significant over- representation of cancer related pathways including glioma especially in the methylation network. This confirms the strong link between methylation and glioblastomas. Potential glioma suppressor genes ACCN3 and ACCN4 linked to NBPF1 neuroblastoma breakpoint family have been identified in our expression network. Numerous ABC transporter genes (ABCA1, ABCB1) present in the expression network suggest drug resistance of glioblastoma tumors.