Differential network analysis reveals the genome-wide landscape of estrogen receptor modulation in hormonal cancers
Journal
Scientific Reports
Journal Volume
6
Date Issued
2016
Author(s)
Hsiao T.-H.
Chiu Y.-C.
Hsu P.-Y.
Tsai M.-H.
Huang T.H.-M.
Chuang E.Y.
Chen Y.
Abstract
Several mutual information (MI)-based algorithms have been developed to identify dynamic gene-gene and function-function interactions governed by key modulators (genes, proteins, etc.). Due to intensive computation, however, these methods rely heavily on prior knowledge and are limited in genome-wide analysis. We present the modulated gene/gene set interaction (MAGIC) analysis to systematically identify genome-wide modulation of interaction networks. Based on a novel statistical test employing conjugate Fisher transformations of correlation coefficients, MAGIC features fast computation and adaption to variations of clinical cohorts. In simulated datasets MAGIC achieved greatly improved computation efficiency and overall superior performance than the MI-based method. We applied MAGIC to construct the estrogen receptor (ER) modulated gene and gene set (representing biological function) interaction networks in breast cancer. Several novel interaction hubs and functional interactions were discovered. ER+ dependent interaction between TGFβ and NFκB was further shown to be associated with patient survival. The findings were verified in independent datasets. Using MAGIC, we also assessed the essential roles of ER modulation in another hormonal cancer, ovarian cancer. Overall, MAGIC is a systematic framework for comprehensively identifying and constructing the modulated interaction networks in a whole-genome landscape. MATLAB implementation of MAGIC is available for academic uses at https://github.com/chiuyc/MAGIC.
SDGs
Other Subjects
estrogen receptor; algorithm; biology; breast tumor; female; gene expression profiling; gene expression regulation; gene regulatory network; genetics; genome-wide association study; human; human genome; Internet; metabolism; ovary tumor; procedures; reproducibility; survival analysis; Algorithms; Breast Neoplasms; Computational Biology; Female; Gene Expression Profiling; Gene Expression Regulation, Neoplastic; Gene Regulatory Networks; Genome, Human; Genome-Wide Association Study; Humans; Internet; Ovarian Neoplasms; Receptors, Estrogen; Reproducibility of Results; Survival Analysis
Publisher
Nature Publishing Group
Type
journal article