Knowledge Management System of Northwest Institute of Plateau Biology, CAS
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 | |
2017-12-22 | |
发表期刊 | ONCOTARGET |
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. |
出版者 | IMPACT JOURNALS LLC |
文献类型 | 期刊论文 |
条目标识符 | http://210.75.249.4/handle/363003/28883 |
专题 | 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). |
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