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- Title
A Systemic Analysis of Transcriptomic and Epigenomic Data To Reveal Regulation Patterns for Complex Disease.
- Authors
Chao Xu; Ji-Gang Zhang; Dongdong Lin; Lan Zhang; Hui Shen; Hong-Wen Deng
- Abstract
Integrating diverse genomics data can provide a global view of the complex biological processes related to the human complex diseases. Although substantial efforts have been made to integrate different omics data, there ate at least three challenges for multi-omics integration methods: (i) How to simultaneously consider the effects of various genomic factors, since these factors jointly influence the phenotypes; (ii) How to effectively incorporate the information from publicly accessible databases and omics datasets to fully capture the interactions among (epi)genomic factors from diverse omics data; and (iii) Until present, the combination of mote than two omics datasets has been poorly explored. Current integration approaches ate not sufficient to address all of these challenges together We proposed a novel integrative analysis framework by incorporating sparse model, multivariate analysis, Gaussian graphical model, and network analysis to address these three challenges simultaneously. Based on this strategy, we perfumed a systemic analysis for glioblastoma multiforme (GDM) integrating genome-wide gene expression, DNA methylation, and miRNA expression data. We identified three regulatory modules of genomic factors associated with GDM survival time and revealed a global regulatory pattern for GDM by combining the three modules, with respect to the common regulatory factors. Out method can not only identify disease-associated dysregulated genomic factors from different omics, but mote importantly, it can incorporate the information from publicly accessible databases and omics datasets to infer a comprehensive interaction map of all these dysregulated genomic factors. Out work represents an innovative approach to enhance out undemanding of molecular genomic mechanisms underlying human complex diseases.
- Subjects
GENOMICS; DATABASES; GLIOBLASTOMA multiforme; MICRORNA; GAUSSIAN function
- Publication
G3: Genes | Genomes | Genetics, 2017, Vol 7, Issue 7, p2271
- ISSN
2160-1836
- Publication type
Article
- DOI
10.1534/g3.117.042408