Construction of a lncRNA-mediated feed-forward loop network reveals global topological features and prognostic motifs in human cancers.

Abstract

Long non-coding RNAs (lncRNAs), transcription factors and microRNAs can form lncRNA-mediated feed-forward loops (L-FFLs), which are functional network motifs that regulate a wide range of biological processes, such as development and carcinogenesis. However, L-FFL network motifs have not been systematically identified, and their roles in human cancers are largely unknown. In this study, we computationally integrated data from multiple sources to construct a global L-FFL network for six types of human cancer and characterized the topological features of the network. Our approach revealed several dysregulated L-FFL motifs common across different cancers or specific to particular cancers. We also found that L-FFL motifs can take part in other types of regulatory networks, such as mRNA-mediated FFLs and ceRNA networks, and form the more complex networks in human cancers. In addition, survival analyses further indicated that L-FFL motifs could potentially serve as prognostic biomarkers. Collectively, this study elucidated the roles of L-FFL motifs in human cancers, which could be beneficial for understanding cancer pathogenesis and treatment.

• Authors: Shangwei Ning, Yue Gao, Peng Wang, Xiang Li, Hui Zhi, Yan Zhang, Yue Liu, Jizhou Zhang, Maoni Guo, Dong Han, Xia Li
• Journal: Oncotarget (Oncotarget) Vol. 7 Issue 29 Pg. 45937-45947 (Jul 19 2016) ISSN: 1949-2553 [Electronic] United States
• PMID: 27322142 (Publication Type: Journal Article)

Chemical References

• Biomarkers, Tumor
• MicroRNAs
• RNA, Long Noncoding
• Transcription Factors

Topics

• Biomarkers, Tumor (genetics)
• Gene Expression Profiling
• Gene Regulatory Networks (genetics)
• Humans
• Kaplan-Meier Estimate
• MicroRNAs (genetics)
• Neoplasms (genetics, mortality)
• Prognosis
• RNA, Long Noncoding (genetics)
• Transcription Factors (genetics)
• Transcriptome