Molecular Network-Based Identification of Competing Endogenous RNAs in Thyroid Carcinoma
Open accessAbstract
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.
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Several researches proved that coding genes, noncoding RNAs, and proteins are related to diseases, including AD.
“Several researches proved that coding genes/noncoding RNAs/proteins were related to diseases, including AD [29,30,31,32,33,34,35,36].”
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An Efficient Classifier for Alzheimer’s Disease Genes Identification
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- Authors
- Lu, M., Xu, X., Xi, B., Dai, Q., Li, C., Su, L., Zhou, X., Tang, M., Yao, Y., & Yang, J.
- Affiliations
- Zhejiang Sci-Tech University (CN)
- Hainan Normal University (CN)
- Wannan Medical College (CN)
- Icahn School of Medicine at Mount Sinai (US)
- Corresponding author
- Yao, Yuhua
- Yang, Jialiang
- Venue
- Genes
- Publisher
- MDPI AG
- Published
- 2018-01-19
- Volume
- 9
- Issue
- 1
- Pages
- 44
- ISSN
- 2073-4425 (ISSN-L)
- PMC
- PMC5793195
- OpenAlex
- W2788158283
- Cited by
- 25
- References
- 93
- Citations by year
- 2025: 1 · 2022: 5 · 2021: 5 · 2020: 1 · 2019: 9 · 2018: 4
- FWCI
- 1.44
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Genes (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- the National Natural Science Foundation of China (61762035)
- the Zhejiang Provincial Natural Science Foundation of China (LY18F020027)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer-related molecular mechanisms research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › MicroRNA in disease regulation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Circular RNAs in diseases
- Keywords
- competing endogenous RNA, thyroid cancer, long non-coding RNA, differentially expressed genes, Runx2, DUSP6, SEMA3D, patient survival, therapeutic biomarkers
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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