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Genes 2018, 9(1), 44; https://doi.org/10.3390/genes9010044

Molecular Network-Based Identification of Competing Endogenous RNAs in Thyroid Carcinoma

1
College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China
2
School of Mathematics and Statistics, Hainan Normal University, Haikou 570100, China
3
Institute of Basic Medical Sciences, Wannan Medical College, Hefei 241000, China
4
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
These authors contributed equally to this study.
*
Authors to whom correspondence should be addressed.
Received: 12 December 2017 / Revised: 10 January 2018 / Accepted: 11 January 2018 / Published: 19 January 2018
(This article belongs to the Special Issue Computational Approaches for Disease Gene Identification)
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Abstract

RNAs may act as competing endogenous RNAs (ceRNAs), a critical mechanism in determining gene expression regulations in many cancers. However, the roles of ceRNAs in thyroid carcinoma remains elusive. In this study, we have developed a novel pipeline called Molecular Network-based Identification of ceRNA (MNIceRNA) to identify ceRNAs in thyroid carcinoma. MNIceRNA first constructs micro RNA (miRNA)–messenger RNA (mRNA)long non-coding RNA (lncRNA) networks from miRcode database and weighted correlation network analysis (WGCNA), based on which to identify key drivers of differentially expressed RNAs between normal and tumor samples. It then infers ceRNAs of the identified key drivers using the long non-coding competing endogenous database (lnCeDB). We applied the pipeline into The Cancer Genome Atlas (TCGA) thyroid carcinoma data. As a result, 598 lncRNAs, 1025 mRNAs, and 90 microRNA (miRNAs) were inferred to be differentially expressed between normal and thyroid cancer samples. We then obtained eight key driver miRNAs, among which hsa-mir-221 and hsa-mir-222 were key driver RNAs identified by both miRNA–mRNA–lncRNA and WGCNA network. In addition, hsa-mir-375 was inferred to be significant for patients’ survival with 34 associated ceRNAs, among which RUNX2, DUSP6 and SEMA3D are known oncogenes regulating cellular proliferation and differentiation in thyroid cancer. These ceRNAs are critical in revealing the secrets behind thyroid cancer progression and may serve as future therapeutic biomarkers. View Full-Text
Keywords: competing endogenous RNA; long non-coding RNA; regulatory network; WGCNA; differentially expressed RNAs; thyroid carcinoma competing endogenous RNA; long non-coding RNA; regulatory network; WGCNA; differentially expressed RNAs; thyroid carcinoma
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Lu, M.; Xu, X.; Xi, B.; Dai, Q.; Li, C.; Su, L.; Zhou, X.; Tang, M.; Yao, Y.; Yang, J. Molecular Network-Based Identification of Competing Endogenous RNAs in Thyroid Carcinoma. Genes 2018, 9, 44.

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