Dataset Information

Competing endogenous RNA analysis reveals the regulatory potency of circRNA_036186 in HNSCC.

ABSTRACT: This study aimed to characterize circular RNA (circRNA) expression profiles and biological functions in head and neck squamous cell carcinoma (HNSCC). Differentially expressed circRNAs were screened using an Arraystar Human CircRNA Array and verified by reverse transcription-quantitative polymerase chain reaction. Multiple bioinformatics methods and a hypergeometric test were employed to predict the interactions between RNAs and the functional circRNA?microRNA (miRNA)-mRNA axes in HNSCC. As a result, 287 circRNAs and 1,053 mRNAs were determined to be differentially expressed in HNSCC compared with the adjacent tissue. In addition, the expression levels of circRNA_036186 and tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, ? polypeptide (14?3?3?) were identified to be significantly different. A competing endogenous RNA (ceRNA) network was constructed, consisting of 5 circRNAs, 385 miRNAs and 96 mRNAs. Furthermore, we predicted that miR?193b?3p exerts a significant effect on 14?3?3?, and was significantly associated with the Hippo signaling pathway in HNSCC. On the whole, these findings suggest that circRNA_036186 likely regulates 14?3?3? expression by functioning as a ceRNA in the development and progression of HNSCC.

SUBMITTER: Wang WL

PROVIDER: S-EPMC6086620 | biostudies-literature | 2018 Oct

REPOSITORIES: biostudies-literature

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Competing endogenous RNA analysis reveals the regulatory potency of circRNA_036186 in HNSCC.

Wang Wen-Long WL Yang Zhi Z Zhang Yi-Juan YJ Lu Ping P Ni You-Kang YK Sun Chang-Fu CF Liu Fa-Yu FY

International journal of oncology 20180724 4

This study aimed to characterize circular RNA (circRNA) expression profiles and biological functions in head and neck squamous cell carcinoma (HNSCC). Differentially expressed circRNAs were screened using an Arraystar Human CircRNA Array and verified by reverse transcription-quantitative polymerase chain reaction. Multiple bioinformatics methods and a hypergeometric test were employed to predict the interactions between RNAs and the functional circRNA‑microRNA (miRNA)-mRNA axes in HNSCC. As a re ...[more]

PMID: 30066847

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Project description:The present study aimed to screen all types of RNAs involved in the development of papillary thyroid carcinoma (PTC). RNA?sequencing data of PTC and normal samples were used for screening differentially expressed (DE) microRNAs (DE?miRNAs), long non?coding RNAs (DE?lncRNAs) and genes (DEGs). Subsequently, lncRNA?miRNA, miRNA?gene (that is, miRNA?mRNA) and gene?gene interaction pairs were extracted and used to construct regulatory networks. Feature genes in the miRNA?mRNA network were identified by topological analysis and recursive feature elimination analysis. A support vector machine (SVM) classifier was built using 15 feature genes, and its classification effect was validated using two microarray data sets that were downloaded from the Gene Expression Omnibus (GEO) database. In addition, Gene Ontology function and Kyoto Encyclopedia Genes and Genomes pathway enrichment analyses were conducted for genes identified in the ceRNA network. A total of 506 samples, including 447 tumor samples and 59 normal samples, were obtained from The Cancer Genome Atlas (TCGA); 16 DE?lncRNAs, 917 DEGs and 30 DE?miRNAs were screened. The miRNA?mRNA regulatory network comprised 353 nodes and 577 interactions. From these data, 15 feature genes with high predictive precision (>95%) were extracted from the network and were used to form an SVM classifier with an accuracy of 96.05% (486/506) for PTC samples downloaded from TCGA, and accuracies of 96.81 and 98.46% for GEO downloaded data sets. The ceRNA regulatory network comprised 596 lines (or interactions) and 365 nodes. Genes in the ceRNA network were significantly enriched in 'neuron development', 'differentiation', 'neuroactive ligand?receptor interaction', 'metabolism of xenobiotics by cytochrome P450', 'drug metabolism' and 'cytokine?cytokine receptor interaction' pathways. Hox transcript antisense RNA, miRNA?206 and kallikrein?related peptidase 10 were nodes in the ceRNA regulatory network of the selected feature gene, and they may serve import roles in the development of PTC.

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Competing endogenous RNA analysis reveals the regulatory potency of circRNA_036186 in HNSCC.

Publications

Competing endogenous RNA analysis reveals the regulatory potency of circRNA_036186 in HNSCC.

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