Identification of cancer prognosis-associated functional modules using differential co-expression networks

	Identification of cancer prognosis-associated functional modules using differential co-expression networks
	Yu, Wenshuai ; Zhao, Shengjie ; Wang, Yongcui ; Zhao, Brian Nlong ; Zhao, Weiling ; Zhou, Xiaobo
刊名	ONCOTARGET
	2017-12-22
英文摘要	The rapid accumulation of cancer-related data owing to high-throughput technologies has provided unprecedented choices to understand the progression of cancer and discover functional networks in multiple cancers. Establishment of co-expression networks will help us to discover the systemic properties of carcinogenesis features and regulatory mechanisms of multiple cancers. Here, we proposed a computational workflow to identify differentially co-expressed gene modules across 8 cancer types by using combined gene differential expression analysis methods and a higher-order generalized singular value decomposition. Four co-expression modules were identified; and oncogenes and tumor suppressors were significantly enriched in these modules. Functional enrichment analysis demonstrated the significantly enriched pathways in these modules, including ECM-receptor interaction, focal adhesion and PI3K-Akt signaling pathway. The top-ranked miRNAs (mir-199, mir-29, mir-200) and transcription factors (FOXO4, E2A, NFAT, and MAZ) were identified, which play an important role in deregulating cellular energetics; and regulating angiogenesis and cancer immune system. The clinical significance of the co-expressed gene clusters was assessed by evaluating their predictability of cancer patients' survival. The predictive power of different clusters and subclusters was demonstrated. Our results will be valuable in cancer-related gene function annotation and for the evaluation of cancer patients' prognosis.
内容类型	期刊论文
源URL	[http://ir.nwipb.ac.cn/handle/363003/13304]
专题	西北高原生物研究所_中国科学院西北高原生物研究所
推荐引用方式 GB/T 7714	Yu, Wenshuai,Zhao, Shengjie,Wang, Yongcui,et al. Identification of cancer prognosis-associated functional modules using differential co-expression networks[J]. ONCOTARGET,2017.
APA	Yu, Wenshuai,Zhao, Shengjie,Wang, Yongcui,Zhao, Brian Nlong,Zhao, Weiling,&Zhou, Xiaobo.(2017).Identification of cancer prognosis-associated functional modules using differential co-expression networks.ONCOTARGET.
MLA	Yu, Wenshuai,et al."Identification of cancer prognosis-associated functional modules using differential co-expression networks".ONCOTARGET (2017).