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Journal articles on the topic 'CERNA NETWORK'

Author: Grafiati

Published: 11 September 2023

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1

Qi, Xin, Yuxin Lin, Jiajia Chen, and Bairong Shen. "Decoding competing endogenous RNA networks for cancer biomarker discovery." Briefings in Bioinformatics 21, no. 2 (2019): 441–57. http://dx.doi.org/10.1093/bib/bbz006.

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Abstract Crosstalk between competing endogenous RNAs (ceRNAs) is mediated by shared microRNAs (miRNAs) and plays important roles both in normal physiology and tumorigenesis; thus, it is attractive for systems-level decoding of gene regulation. As ceRNA networks link the function of miRNAs with that of transcripts sharing the same miRNA response elements (MREs), e.g. pseudogenes, competing mRNAs, long non-coding RNAs, and circular RNAs, the perturbation of crucial interactions in ceRNA networks may contribute to carcinogenesis by affecting the balance of cellular regulatory system. Therefore, d

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Hsiao, Yi-Wen, Lin Wang, and Tzu-Pin Lu. "ceRNAR: An R package for identification and analysis of ceRNA-miRNA triplets." PLOS Computational Biology 18, no. 9 (2022): e1010497. http://dx.doi.org/10.1371/journal.pcbi.1010497.

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Competitive endogenous RNA (ceRNA) represents a novel mechanism of gene regulation that controls several biological and pathological processes. Recently, an increasing number of in silico methods have been developed to accelerate the identification of such regulatory events. However, there is still a need for a tool supporting the hypothesis that ceRNA regulatory events only occur at specific miRNA expression levels. To this end, we present an R package, ceRNAR, which allows identification and analysis of ceRNA-miRNA triplets via integration of miRNA and RNA expression data. The ceRNAR package

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Jayarathna, Dulari K., Miguel E. Rentería, Emilie Sauret, Jyotsna Batra, and Neha S. Gandhi. "Identifying Complex lncRNA/Pseudogene–miRNA–mRNA Crosstalk in Hormone-Dependent Cancers." Biology 10, no. 10 (2021): 1014. http://dx.doi.org/10.3390/biology10101014.

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The discovery of microRNAs (miRNAs) has fundamentally transformed our understanding of gene regulation. The competing endogenous RNA (ceRNA) hypothesis postulates that messenger RNAs and other RNA transcripts, such as long non-coding RNAs and pseudogenes, can act as natural miRNA sponges. These RNAs influence each other’s expression levels by competing for the same pool of miRNAs through miRNA response elements on their target transcripts, thereby modulating gene expression and protein activity. In recent years, these ceRNA regulatory networks have gained considerable attention in cancer resea

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Chen, Chen, Li Wang, Qiuju Feng, Qi Liu, Li Wang, and Shuming Huang. "Comprehensive Landscape of Modules-Dysregulated Functions Reveals a Profound Role of ceRNAs in Coronary Heart Disease." Journal of Healthcare Engineering 2022 (March 8, 2022): 1–10. http://dx.doi.org/10.1155/2022/4547413.

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Coronary heart disease (CHD) is one of the most common severe cardiovascular diseases. Competitive endogenous RNAs (ceRNA) play critical roles in complex diseases. However, our understanding of the dysregulated functions of ceRNAs in CHD remains limited. Here, we systematically analyzed the alterations of ceRNAs and identified the specific functions based on dysregulated modules from the ceRNA network. A total of 2457 significantly differential expressed genes and 212 differential expressed lncRNAs were identified. We got 76679 regulator relationship between different expression genes and miRN

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Liang, Ying-Chun, Yu-Peng Wu, Dong-Ning Chen, et al. "Building a Competing Endogenous RNA Network to Find Potential Long Non-Coding RNA Biomarkers for Pheochromocytoma." Cellular Physiology and Biochemistry 51, no. 6 (2018): 2916–24. http://dx.doi.org/10.1159/000496043.

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Background/Aims: Accumulating evidence has shown that long non-coding RNAs (lncRNAs) in competing endogenous RNA (ceRNA) networks play crucial roles in tumor survival and patient prognosis; however, studies investigating ceRNA networks in pheochromocytoma (PCC) are lacking. In this study, we investigated the pathogenesis of PCC and whether lncRNAs acting through ceRNAs networks were associated with prognosis. Methods: A total of 183 PCC samples and 3 control samples from The Cancer Genome Atlas database were analyzed. The Empirical Analysis of Digital Gene Expression Data package in R (edgeR)

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Ye, Hongwei, Yuping Li, Lu Li, Yuhui Huang, Jiahui Wang, and Qin Gao. "Construction of a ceRNA network of regulated ferroptosis in doxorubicin-induced myocardial injury." PeerJ 11 (January 25, 2023): e14767. http://dx.doi.org/10.7717/peerj.14767.

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Background Ferroptosis and long-noncoding RNAs (lncRNAs) play crucial roles in doxorubicin (DOX)-induced myocardial injury (DIMI). Nevertheless, there is no research to construct competing endogenous RNAs (ceRNAs) network between lncRNAs and ferroptosis-related key gene. So our research was designed to screen ferroptosis-related genes from differentially expressed mRNAs in DIMI and construct lncRNAs regulated ferroptosis-related key gene ceRNAs network. Methods The male mice were injected with DOX intraperitoneally to induce myocardial injury, myocardial injury was evaluated by hematoxylin and

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Sheng, Han, Huan Pan, Ming Yao, et al. "Integrated Analysis of Circular RNA-Associated ceRNA Network Reveals Potential circRNA Biomarkers in Human Breast Cancer." Computational and Mathematical Methods in Medicine 2021 (December 20, 2021): 1–16. http://dx.doi.org/10.1155/2021/1732176.

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Circular RNA (circRNA) is closely related to tumorigenesis and cancer progression. Yet, the roles of cancer-specific circRNAs in the circRNA-related ceRNA network of breast cancer (BRCA) remain unclear. The aim of this study was to construct a ceRNA network associated with circRNA and to explore new therapeutic and prognostic targets and biomarkers for breast cancer. We downloaded the circRNA expression profile of BRCA from Gene Expression Omnibus (GEO) microarray datasets and downloaded the miRNA and mRNA expression profiles of BRCA from The Cancer Genome Atlas (TCGA) database. Differentially

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Wang, Chao, Kunkai Su, Hanchao Lin, Beini Cen, Shusen Zheng, and Xiao Xu. "Identification and Verification of a Novel MAGI2-AS3/miRNA-374-5p/FOXO1 Network Associated with HBV-Related HCC." Cells 11, no. 21 (2022): 3466. http://dx.doi.org/10.3390/cells11213466.

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Background: Hepatocellular carcinoma (HCC) is a very common neoplasm worldwide, and competitive endogenous RNA (ceRNA) plays an important role in the development of HCC. The purpose of this study is to investigate the molecular mechanisms of ceRNAs in HCC. Methods: This study detects potential ceRNAs from HCC through whole genome analysis of lncRNA, miRNA and mRNA expression. We then performed high-throughput sequencing of tissues from five hepatitis B related HCC patients to screen ceRNAs and those screened ceRNAs expressions were verified on tissues from an independent group of six patients.

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An, Biao, Yuan Hu, and Xiao Liang. "Integrated Analysis of the lncRNA-Associated ceRNA Network in Wilms Tumor via TARGET and GEO Databases." Genetics Research 2022 (August 31, 2022): 1–12. http://dx.doi.org/10.1155/2022/2365991.

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Wilms tumor (WT) is the most common genitourinary renal tumor that typically occurs in children under 15 and is thought to be linked to somatic and germline mutations. However, the specific functional role of competing endogenous RNAs (ceRNAs) and their potential implications in WT remain unclear. In this study, we developed an lncRNA-mediated (long noncoding RNA-mediated) ceRNA network via the R packages for WT with expression data obtained from the tumor alterations relevant for genomics-driven therapy (TARGET) database. Unsupervised hierarchical clustering analysis revealed that the WT spec

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Ye, Junhong, Jifu Li, and Ping Zhao. "Roles of ncRNAs as ceRNAs in Gastric Cancer." Genes 12, no. 7 (2021): 1036. http://dx.doi.org/10.3390/genes12071036.

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Although ignored in the past, with the recent deepening of research, significant progress has been made in the field of non-coding RNAs (ncRNAs). Accumulating evidence has revealed that microRNA (miRNA) response elements regulate RNA. Long ncRNAs, circular RNAs, pseudogenes, miRNAs, and messenger RNAs (mRNAs) form a competitive endogenous RNA (ceRNA) network that plays an essential role in cancer and cardiovascular, neurodegenerative, and autoimmune diseases. Gastric cancer (GC) is one of the most common cancers, with a high degree of malignancy. Considerable progress has been made in understa

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Zhang, Senmiao, Yanling Li, Shuyu Xin, et al. "Insight into LncRNA- and CircRNA-Mediated CeRNAs: Regulatory Network and Implications in Nasopharyngeal Carcinoma—A Narrative Literature Review." Cancers 14, no. 19 (2022): 4564. http://dx.doi.org/10.3390/cancers14194564.

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Nasopharyngeal carcinoma (NPC) is a kind of head-and-neck malignant tumor, and distant metastasis treatment resistance is the leading cause of patient death. In-depth understanding of NPC progression and treatment failure remains to be explored. Long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) are noncoding RNAs that play key regulatory role in shaping tumor cell activities. Recent studies have revealed that lncRNA and circRNA function as competitive endogenous RNAs (ceRNAs) by regulating the posttranscriptional expression of genes as miRNA baits. The imbalanced ceRNA networks derive

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Cheng, Yang, Lanlan Geng, Kunyuan Wang, et al. "Long Noncoding RNA Expression Signatures of Colon Cancer Based on the ceRNA Network and Their Prognostic Value." Disease Markers 2019 (March 11, 2019): 1–13. http://dx.doi.org/10.1155/2019/7636757.

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Background. The specific functional roles of long noncoding RNAs (lncRNAs) as ceRNAs in colon cancer and their potential implications for colon cancer prognosis remain unclear. In the present study, a genome-wide analysis was performed to investigate the potential lncRNA-mediated ceRNA interplay in colon cancer based on the “ceRNA hypothesis.” The prognostic value of the lncRNAs was evaluated. Methods. A dysregulated lncRNA-associated ceRNA network was constructed based on the miRNA, lncRNA, and mRNA expression profiles in combination with the miRNA regulatory network by using an integrative c

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Liu, Haiyang, Di Liu, Yexin Liu, et al. "Comprehensive analysis of circRNA expression profiles and circRNA-associated competing endogenous RNA networks in IgA nephropathy." PeerJ 8 (December 3, 2020): e10395. http://dx.doi.org/10.7717/peerj.10395.

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Background Immunoglobulin A nephropathy (IgAN) is immune-mediated primary glomerulonephritis, which is the most common reason leading to renal failure worldwide. The exact pathogenesis of IgAN is not well defined. Accumulating evidence indicates that circular RNAs (circRNAs) play crucial roles in the immune disease by involving in the competing endogenous RNA (ceRNA) network mechanism. At present, the studies of the circRNA profiles and circRNA-associated ceRNA networks in the IgAN are still scarce. This study aimed to elucidate the potential roles of circRNA-associated ceRNA networks of perip

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Zhang, Jin, Fei Xiao, Guangliang Qiang, et al. "Novel lncRNA Panel as for Prognosis in Esophageal Squamous Cell Carcinoma Based on ceRNA Network Mechanism." Computational and Mathematical Methods in Medicine 2021 (September 24, 2021): 1–12. http://dx.doi.org/10.1155/2021/8020879.

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Background. The competitive endogenous RNA (ceRNA) mechanism has been discovered recently and regulating cancer-related gene expressions. The ceRNA network participates in multiple processes, such as cell proliferation and metastasis, and potentially drives the progression of cancer. In this study, we focus on the ceRNA networks of esophageal squamous cell carcinoma and discovered a novel biomarker panel for cancer prognosis. Methods. RNA expression data of esophageal carcinoma from the TCGA database were achieved and constructed ceRNA network in esophageal carcinoma using R packages. Results.

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Li, Ziwen, Xueli An, Taotao Zhu, et al. "Discovering and Constructing ceRNA-miRNA-Target Gene Regulatory Networks during Anther Development in Maize." International Journal of Molecular Sciences 20, no. 14 (2019): 3480. http://dx.doi.org/10.3390/ijms20143480.

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The “competing endogenous RNA (ceRNA) hypothesis” has recently been proposed for a new type of gene regulatory model in many organisms. Anther development is a crucial biological process in plant reproduction, and its gene regulatory network (GRN) has been gradually revealed during the past two decades. However, it is still unknown whether ceRNAs contribute to anther development and sexual reproduction in plants. We performed RNA and small RNA sequencing of anther tissues sampled at three developmental stages in two maize lines. A total of 28,233 stably transcribed loci, 61 known and 51 potent

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Sen, Rituparno, Suman Ghosal, Shaoli Das, Subrata Balti, and Jayprokas Chakrabarti. "Competing Endogenous RNA: The Key to Posttranscriptional Regulation." Scientific World Journal 2014 (2014): 1–6. http://dx.doi.org/10.1155/2014/896206.

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Competing endogenous RNA, ceRNA, vie with messenger RNAs (mRNAs) for microRNAs (miRNAs) with shared miRNAs responses elements (MREs) and act as modulator of miRNA by influencing the available level of miRNA. It has recently been discovered that, apart from protein-coding ceRNAs, pseudogenes, long noncoding RNAs (lncRNAs), and circular RNAs act as miRNA “sponges” by sharing common MRE, inhibiting normal miRNA targeting activity on mRNA. These MRE sharing elements form the posttranscriptional ceRNA network to regulate mRNA expression. ceRNAs are widely implicated in many biological processes. Re

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Guo, Ya, Wei Kang Pan, Zhong Wei Wang, et al. "Identification of Novel Biomarkers for Predicting Prognosis and Immunotherapy Response in Head and Neck Squamous Cell Carcinoma Based on ceRNA Network and Immune Infiltration Analysis." BioMed Research International 2021 (December 6, 2021): 1–42. http://dx.doi.org/10.1155/2021/4532438.

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Objectives. Patients with head and neck squamous cell carcinoma (HNSCC) have poor prognosis and show poor responses to immune checkpoint (IC) inhibitor (ICI) therapy. Competing endogenous RNA (ceRNA) networks, tumor-infiltrating immune cells (TIICs), and ICIs may influence tumor prognosis and response rates to ICI therapy. This study is aimed at identifying prognostic and IC-related biomarkers and key TIIC signatures to improve prognosis and ICI therapy response in HNSCC patients. Methods and Results. Ninety-five long noncoding RNAs (lncRNAs), microRNAs (miRNAs), and 1746 mRNAs were identified

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Wang, Chenxu, Chaofan Yang, Xinying Wang, Guanlun Zhou, Chao Chen, and Guorong Han. "ceRNA Network and Functional Enrichment Analysis of Preeclampsia by Weighted Gene Coexpression Network Analysis." Computational and Mathematical Methods in Medicine 2022 (January 7, 2022): 1–14. http://dx.doi.org/10.1155/2022/5052354.

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Background. Preeclampsia (PE) is a multisystemic syndrome which has short- and long-term risk to mothers and children and has pluralistic etiology. Objective. This study is aimed at constructing a competitive endogenous RNA (ceRNA) network for pathways most related to PE using a data mining strategy based on weighted gene coexpression network analysis (WGCNA). Methods. We focused on pathways involving hypoxia, angiogenesis, and epithelial mesenchymal transition according to the gene set variation analysis (GSVA) scores. The gene sets of these three pathways were enriched by gene set enrichment

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Li, Yueqi, Wudi Wei, Sanqi An, et al. "Identification and analysis of lncRNA, microRNA and mRNA expression profiles and construction of ceRNA network in Talaromyces marneffei-infected THP-1 macrophage." PeerJ 9 (January 13, 2021): e10529. http://dx.doi.org/10.7717/peerj.10529.

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Background Competitive endogenous RNA (ceRNA) reveals new mechanisms for interactions between RNAs, which have been considered to play a significant role in pathogen-host innate immune response. However, knowledge of ceRNA regulatory networks in Talaromyces marneffei (TM)-macrophages is still limited. Methods Next-generation sequencing technology (NGS) was used to obtain mRNA, miRNA and lncRNA expression profiles in TM-infected macrophages. The R package DESeq2 was used to identify differentially expressed lncRNA, miRNA and mRNA. The R package GOseq was used for Gene Ontology (GO) and Kyoto En

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Tan, Juan, Weimin Wang, Bin Song, Yingjian Song, and Zili Meng. "Integrative Analysis of Three Novel Competing Endogenous RNA Biomarkers with a Prognostic Value in Lung Adenocarcinoma." BioMed Research International 2020 (August 4, 2020): 1–12. http://dx.doi.org/10.1155/2020/2837906.

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Increasing evidence has shown competitive endogenous RNAs (ceRNAs) play key roles in numerous cancers. Nevertheless, the ceRNA network that can predict the prognosis of lung adenocarcinoma (LUAD) is still lacking. The aim of the present study was to identify the prognostic value of key ceRNAs in lung tumorigenesis. Differentially expressed (DE) RNAs were identified between LUAD and adjacent normal samples by limma package in R using The Cancer Genome Atlas database (TCGA). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway function enrichment analysis was performed u

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Zhang, Zhiyuan, Wenwei Qian, Sen Wang, et al. "Analysis of lncRNA-Associated ceRNA Network Reveals Potential lncRNA Biomarkers in Human Colon Adenocarcinoma." Cellular Physiology and Biochemistry 49, no. 5 (2018): 1778–91. http://dx.doi.org/10.1159/000493623.

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Background/Aims: Long non-coding RNAs (lncRNAs) acting as competing endogenous RNAs (ceRNAs) play significant roles in the development of tumors, but the functions of specific lncRNAs and lncRNA-related ceRNA networks have not been fully elucidated for colon adenocarcinoma (COAD). In this study, we aimed to clarify the lncRNA-microRNA (miRNA)-mRNA ceRNA network and potential lncRNA biomarkers in COAD. Methods: We extracted data from The Cancer Genome Atlas (TCGA) and identified COAD-specific mRNAs, miRNAs, and lncRNAs. The biological processes in Gene Ontology (GO) and the Kyoto Encyclopedia o

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Dong, Yanru, Weibo Wen, Tiezheng Yuan, Lan Liu, and Xiangdan Li. "Novel Prognostic Biomarkers for Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (CESC) Patients via Analysis of Competing Endogenous RNA (ceRNA) Network." Disease Markers 2023 (February 8, 2023): 1–12. http://dx.doi.org/10.1155/2023/1766080.

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Background. Cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) is a common malignant gynecological cancer. The ceRNA networks play important roles in many tumors, while RILPL2-related ceRNA network has been seldom studied in CESC. Methods. All CESC data was obtained from TCGA database. Differentially expressed RNAs and predicted target RNAs were cross analyzed to construct ceRNA network. RNA and clinicopathological characteristics’ influence on overall survival (OS) were determined by univariate and multivariate Cox regression analyses. Lasso regression was used to constru

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Xu, Junhua, Min Wu, Yichen Sun, Hongqian Zhao, Yujie Wang, and Jie Gao. "Identifying Dysregulated lncRNA-Associated ceRNA Network Biomarkers in CML Based on Dynamical Network Biomarkers." BioMed Research International 2020 (February 18, 2020): 1–8. http://dx.doi.org/10.1155/2020/5189549.

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The incidence of chronic myeloid leukemia (CML) is increasing year by year, which is a serious threat to human health. Early diagnosis can reduce mortality and improve prognosis. LncRNAs have been shown to be effective biomarkers for a variety of diseases and can act as competitive endogenous RNA (ceRNA). In this study, the dysregulated lncRNA-associated ceRNA networks (DLCN) of the chronic phase (CP), accelerated phase (AP), and blastic crisis (BC) for CML are constructed. Then, based on dynamic network biomarkers (DNB), some dysregulated lncRNA-associated ceRNA network biomarkers of CP, AP,

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Liu, Yuehui, and Fan Ye. "Construction and integrated analysis of crosstalking ceRNAs networks in laryngeal squamous cell carcinoma." PeerJ 7 (July 22, 2019): e7380. http://dx.doi.org/10.7717/peerj.7380.

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Background Laryngeal squamous cell carcinoma (LSCC) is one of the most common malignant tumours of the head and neck. Recent evidence has demonstrated that lncRNAs play important roles in tumour progression and could be used as biomarkers for early diagnosis, prognosis, and potential therapeutic targets. The “competitive endogenous RNA (ceRNA)” hypothesis states that lncRNAs competitively bind to miRNAs through their intramolecular miRNA reaction elements (MREs) to construct a wide range of ceRNA regulatory networks. This study aims to predict the role of ceRNA network in LSCC, for advancing t

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Fiscon, Giulia, Federica Conte, Lorenzo Farina, and Paola Paci. "Network-Based Approaches to Explore Complex Biological Systems towards Network Medicine." Genes 9, no. 9 (2018): 437. http://dx.doi.org/10.3390/genes9090437.

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Network medicine relies on different types of networks: from the molecular level of protein–protein interactions to gene regulatory network and correlation studies of gene expression. Among network approaches based on the analysis of the topological properties of protein–protein interaction (PPI) networks, we discuss the widespread DIAMOnD (disease module detection) algorithm. Starting from the assumption that PPI networks can be viewed as maps where diseases can be identified with localized perturbation within a specific neighborhood (i.e., disease modules), DIAMOnD performs a systematic anal

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Zhou, Dongkai, Bingqiang Gao, Qifan Yang, Yang Kong, and Weilin Wang. "Integrative Analysis of ceRNA Network Reveals Functional lncRNAs in Intrahepatic Cholangiocarcinoma." BioMed Research International 2019 (November 25, 2019): 1–9. http://dx.doi.org/10.1155/2019/2601271.

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Intrahepatic cholangiocarcinoma (ICC) is the second most common lethal liver cancer worldwide. Currently, despite the latest developments in genomics and transcriptomics for ICC in recent years, the molecular pathogenesis promoting ICC remains elusive, especially in regulatory mechanisms of long noncoding RNAs (lncRNAs), which acts as competing endogenous RNA (ceRNA). In order to elucidate the molecular mechanism of functional lncRNA, expression profiles of lncRNAs, microRNAs (miRNAs), and messenger RNAs (mRNAs) were obtained from The Cancer Genome Atlas (TCGA) database and an integrative anal

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Luo, Liang, Lei-Lei Zhang, Wen Tao, Tao-Lin Xia, and Liao-Yuan Li. "Prediction of potential prognostic biomarkers in metastatic prostate cancer based on a circular RNA-mediated competing endogenous RNA regulatory network." PLOS ONE 16, no. 12 (2021): e0260983. http://dx.doi.org/10.1371/journal.pone.0260983.

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Recently, studies on competing endogenous RNA (ceRNA) networks have become prevalent, and circular RNAs (circRNAs) have crucial implications for the development and progression of carcinoma. However, studies relevant to metastatic prostate cancer (mPCa) are scant. This study aims to discover potential ceRNAs that may be related to the prognosis of mPCa. RNA-Seq data were obtained from the MiOncoCirc database and Gene Expression Omnibus (GEO). Differential expression patterns of RNAs were examined using R packages. Circular RNA Interactome, miRTarBase, miRDB and TargetScan were applied to predi

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Wang, Yuanyong, Tong Lu, Yang Wo, et al. "Identification of a putative competitive endogenous RNA network for lung adenocarcinoma using TCGA datasets." PeerJ 7 (April 23, 2019): e6809. http://dx.doi.org/10.7717/peerj.6809.

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The mechanisms underlying the oncogenesis and progression of lung adenocarcinoma (LUAD) are currently unclear. The discovery of competitive endogenous RNA (ceRNA) regulatory networks has provided a new direction for the treatment and prognosis of patients with LUAD. However, the mechanism of action of ceRNA in LUAD remains elusive. In the present study, differentially expressed mRNAs, microRNAs (miRs) and long non-coding RNAs from the cancer genome atlas database were screened. CeRNAs for LUAD were then identified using online prediction software. Among the ceRNAs identified, family with seque

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Bo, Hao, Zhizhong Liu, Fang Zhu, et al. "Long noncoding RNAs expression profile and long noncoding RNA-mediated competing endogenous RNA network in nonobstructive azoospermia patients." Epigenomics 12, no. 8 (2020): 673–84. http://dx.doi.org/10.2217/epi-2020-0008.

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Aim: To analyze the expression profile and competing endogenous RNA (ceRNA) network of long noncoding RNAs (lncRNAs) in nonobstructive azoospermia (NOA). Materials & methods: The lncRNA expression profile in NOA was determined by microarray reanalysis. Differential expression analysis was performed by R software. The ceRNA network was constructed using correlation analysis and gene target miRNA prediction. Metascape was used for enrichment analysis. Again ceRNA network was validated by quantitative real-time PCR. Results: Many lncRNAs are differently expressed in NOA. LncRNAs might partici

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Liu, Xiu-Juan, Hong-Lin Yin, Yan Li, Hao Hao, Yang Liu, and Quan-Lin Zhao. "The Construction and Analysis of a ceRNA Network Related to Salt-Sensitivity Hypertensives." BioMed Research International 2022 (October 14, 2022): 1–14. http://dx.doi.org/10.1155/2022/8258351.

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Background. Salt-sensitivity hypertensives (SSH) are an independent risk factor for cardiovascular disease. However, the mechanism of SSH is not clear. This study is aimed at constructing a competing endogenous RNA (ceRNA) network related to SSH. Methods. Data sets were collected from the Gene Expression Omnibus database (GEO) to extract data on salt sensitivity RNA of patients with or without hypertensives in GSE135111. Firstly, we analyzed differentially expressed genes (DEGs, log 2 FC ≥ 0.5 and P < 0.05 ) and differentially expressed lncRNAs (DELs, log2FC ≥1 and P<0.05) between SSH an

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Luo, Zhiwen, and Xinyu Bi. "Effect of an lncRNA-associated ceRNA regulatory network in MVI-positive hepatocellular carcinoma on their sensitivity to sorafenib." Journal of Clinical Oncology 38, no. 15_suppl (2020): e16615-e16615. http://dx.doi.org/10.1200/jco.2020.38.15_suppl.e16615.

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e16615 Background: Microvascular invasion (MVI) is a histological feature of hepatocellular carcinoma (HCC) related to aggressiveness. But different sensitivity to first line targeted drug, sorafenib, in MVI+ HCC has been observed. Long noncoding RNAs (lncRNAs) can act as microRNA (miRNA) sponges to regulate protein-coding gene expression; so lncRNAs are considered as a major part of competitive endogenous RNA (ceRNA) network and have attracted growing attention. We explored the regulatory mechanisms and functional roles of lncRNAs as ceRNAs in MVI+ HCC, and ceRNA network’s potential impact on

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Kim, Nam Hee, Sang Hyun Song, Yun Hee Choi, et al. "Competing Endogenous RNA of Snail and Zeb1 UTR in Therapeutic Resistance of Colorectal Cancer." International Journal of Molecular Sciences 22, no. 17 (2021): 9589. http://dx.doi.org/10.3390/ijms22179589.

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The epithelial-mesenchymal transition (EMT) comprises an important biological mechanism not only for cancer progression but also in the therapeutic resistance of cancer cells. While the importance of the protein abundance of EMT-inducers, such as Snail (SNAI1) and Zeb1 (ZEB1), during EMT progression is clear, the reciprocal interactions between the untranslated regions (UTRs) of EMT-inducers via a competing endogenous RNA (ceRNA) network have received little attention. In this study, we found a synchronized transcript abundance of Snail and Zeb1 mediated by a non-coding RNA network in colorect

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Chen, Lixian, Zhonglu Ren, and Yongming Cai. "Construction and Analysis of Survival-Associated Competing Endogenous RNA Network in Lung Adenocarcinoma." BioMed Research International 2021 (February 11, 2021): 1–17. http://dx.doi.org/10.1155/2021/4093426.

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Increasing evidence has shown that noncoding RNAs play significant roles in the initiation, progression, and metastasis of tumours via participating in competing endogenous RNA (ceRNA) networks. However, the survival-associated ceRNA in lung adenocarcinoma (LUAD) remains poorly understood. In this study, we aimed to investigate the regulatory mechanisms underlying ceRNA in LUAD to identify novel prognostic factors. mRNA, lncRNA, and miRNA sequencing data obtained from the GDC data portal were utilized to identify differentially expressed (DE) RNAs. Survival-related RNAs were recognized using u

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Li, Jianxin, Xin Wang, Yinchun Wang, and Qingqiang Yang. "H19 promotes the gastric carcinogenesis by sponging miR-29a-3p: evidence from lncRNA–miRNA–mRNA network analysis." Epigenomics 12, no. 12 (2020): 989–1002. http://dx.doi.org/10.2217/epi-2020-0114.

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Aim: To identify novel competing endogenous RNA (ceRNA) network correlated with the prognosis of gastric cancer (GC) patients. Materials & methods: We systematically analyzed the aberrantly expressed genes in human GC to construct a ceRNA network by using multiple bioinformatic tools. Results: Aberrantly expressed mRNAs in GC were identified. By means of stepwise reverse prediction and validation from mRNA to lncRNA, a ceRNA network comprised of H19, miR-29a-3p, COL3A1, COL5A2, COL1A2 and COL4A1 was constructed, and all genes in the network are significantly correlated with the prognosis o

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Ari Yuka, Selcen, and Alper Yilmaz. "Effect of SARS-CoV-2 infection on host competing endogenous RNA and miRNA network." PeerJ 9 (October 20, 2021): e12370. http://dx.doi.org/10.7717/peerj.12370.

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Competing endogenous RNAs (ceRNA) play a crucial role in cell functions. Computational methods that provide large-scale analysis of the interactions between miRNAs and their competitive targets can contribute to the understanding of ceRNA regulations and critical regulatory functions. Recent reports showed that viral RNAs can compete with host RNAs against host miRNAs. Regarding SARS-CoV-2 RNA, no comprehensive study had been reported about its competition with cellular ceRNAs. In this study, for the first time, we used the ceRNAnetsim package to assess ceRNA network effects per individual cel

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Xu, Jingxi, and Jiangtao Li. "Construction of a three commitment points for S phase entry cell cycle model and immune-related ceRNA network to explore novel therapeutic options for psoriasis." Mathematical Biosciences and Engineering 19, no. 12 (2022): 13483–525. http://dx.doi.org/10.3934/mbe.2022630.

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<abstract> <p>While competing endogenous RNAs (ceRNAs) play pivotal roles in various diseases, the proliferation and differentiation of keratinocytes are becoming a research focus in psoriasis. Therefore, the three commitment points for S phase entry (CP1–3) cell cycle model has pointed to a new research direction in these areas. However, it is unclear what role ceRNA regulatory mechanisms play in the interaction between keratinocytes and the immune system in psoriasis. In addition, the ceRNA network-based screening of potential therapeutic agents for psoriasis has not been explore

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Mao, Jia, Yufei Zhou, Licheng Lu, et al. "Identifying a Serum Exosomal-Associated lncRNA/circRNA-miRNA-mRNA Network in Coronary Heart Disease." Cardiology Research and Practice 2021 (June 23, 2021): 1–10. http://dx.doi.org/10.1155/2021/6682183.

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Background. Accumulating evidence supports the importance of noncoding RNAs and exosomes in coronary heart disease (CHD). However, exosomal-associated competing endogenous RNA- (ceRNA-) mediated regulatory mechanisms in CHD are largely unexplored. The present study aimed to explore exosomal-associated ceRNA networks in CHD. Methods. Data from 6 CHD patients and 32 normal controls were downloaded from the ExoRBase database. CHD and normal controls were compared by screening differentially expressed mRNAs (DEMs), lncRNAs (DELs), and circRNAs (DECs) in serum exosomes. MicroRNAs (miRNAs) targeting

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Han, Xueqiong, Jianxun Lu, Chun Chen, et al. "Seven Hub Genes Predict the Prognosis of Hepatocellular Carcinoma and the Corresponding Competitive Endogenous RNA Network." Journal of Oncology 2022 (October 12, 2022): 1–14. http://dx.doi.org/10.1155/2022/3379330.

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Purpose. This study was aimed at identifying hub genes and ceRNA regulatory networks linked to prognosis in hepatocellular carcinoma (HCC) and to identify possible therapeutic targets. Methods. Differential expression analyses were performed to detect the differentially expressed genes (DEGs) in the four datasets (GSE76427, GSE6764, GSE62232, and TCGA). The intersected DEmRNAs were identified to explore biological significance by enrichment analysis. We built a competitive endogenous RNA (ceRNA) network of lncRNA-miRNA-mRNA. The mRNAs of the ceRNA network were used to perform Cox and Kaplan-Me

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List, Markus, Azim Dehghani Amirabad, Dennis Kostka, and Marcel H. Schulz. "Large-scale inference of competing endogenous RNA networks with sparse partial correlation." Bioinformatics 35, no. 14 (2019): i596—i604. http://dx.doi.org/10.1093/bioinformatics/btz314.

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AbstractMotivationMicroRNAs (miRNAs) are important non-coding post-transcriptional regulators that are involved in many biological processes and human diseases. Individual miRNAs may regulate hundreds of genes, giving rise to a complex gene regulatory network in which transcripts carrying miRNA binding sites act as competing endogenous RNAs (ceRNAs). Several methods for the analysis of ceRNA interactions exist, but these do often not adjust for statistical confounders or address the problem that more than one miRNA interacts with a target transcript.ResultsWe present SPONGE, a method for the f

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Song, Yueqiang, Jia Li, Yiming Mao, and Xi Zhang. "ceRNAshiny: An Interactive R/Shiny App for Identification and Analysis of ceRNA Regulation." Frontiers in Molecular Biosciences 9 (May 13, 2022). http://dx.doi.org/10.3389/fmolb.2022.865408.

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The competing endogenous RNA (ceRNA) network is a newly discovered post-transcriptional regulation that controls both physiological and pathological progresses. Increasing research studies have been pivoted on this theory to explore the function of novel non-coding RNAs, pseudogenes, circular RNAs, and messenger RNAs. Although there are several R packages or computational tools to analyze ceRNA networks, an urgent need for easy-to-use computational tools still remains to identify ceRNA regulation. Besides, the conventional tools were mainly devoted to investigating ceRNAs in malignancies inste

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Huang, Runzhi, Ziqi Liu, Tingli Tian, et al. "The construction and analysis of tumor-infiltrating immune cells and ceRNA networks in metastatic adrenal cortical carcinoma." Bioscience Reports 40, no. 3 (2020). http://dx.doi.org/10.1042/bsr20200049.

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Abstract Purpose: To construct and analyze tumor-infiltrating immune cell and ceRNA (competitive endogenous RNA) networks in metastatic adrenal cortical carcinoma (ACC). Methods: A ceRNA network was established to identify the ceRNAs involved in metastasis of ACC based on 92 samples from TCGA, including 18 cases of metastasis and 74 cases of non-metastatic primary tumors. And the algorithm “cell type identification by estimating relative subsets of RNA transcripts (CIBERSORT)” was used to quantify the proportion of immune cells in ACC. In addition, predictive nomograms based on the types of im

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Wang, Peng, Xin Li, Yue Gao, et al. "LnCeVar: a comprehensive database of genomic variations that disturb ceRNA network regulation." Nucleic Acids Research, October 16, 2019. http://dx.doi.org/10.1093/nar/gkz887.

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Abstract LnCeVar (http://www.bio-bigdata.net/LnCeVar/) is a comprehensive database that aims to provide genomic variations that disturb lncRNA-associated competing endogenous RNA (ceRNA) network regulation curated from the published literature and high-throughput data sets. LnCeVar curated 119 501 variation–ceRNA events from thousands of samples and cell lines, including: (i) more than 2000 experimentally supported circulating, drug-resistant and prognosis-related lncRNA biomarkers; (ii) 11 418 somatic mutation–ceRNA events from TCGA and COSMIC; (iii) 112 674 CNV–ceRNA events from TCGA; (iv) 6

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Zhong, Yinming, Sicen Pan, Shunji Zhi, et al. "Construction and investigation of circRNA-associated ceRNA regulatory network in molecular subtypes of breast cancer." Current Computer-Aided Drug Design 18 (June 15, 2022). http://dx.doi.org/10.2174/1573409918666220615151614.

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Background: Circular RNAs (circRNAs) act as competing endogenous RNAs (ceRNAs) that indirectly regulate gene expression and function by binding microRNAs (miRNAs). A growing body of evidence indicates that the ceRNA networks can be used as an effective method to investigate cancer; however, the construction and analysis of ceRNA networks, especially circRNA-miRNA-mRNA regulatory network, in different subtypes of breast cancer has not been previously performed. Methods: First, the expression profiles of circRNA, miRNA, and mRNA were downloaded from the GEO database, differentially expressed gen

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Wang, Jing, and Jie Li. "LncRNA MIR155HG functions as a ceRNA for inhibition of lung adenocarcinoma growth and prediction of prognosis." Archives of Medical Science, February 9, 2021. http://dx.doi.org/10.5114/aoms/131198.

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IntroductionLong non-coding RNAs (lncRNAs) functioning as competing endogenous RNAs (ceRNAs) play critical roles in tumour progression. However, prognosis-related ceRNA networks in lung adenocarcinoma (LUAD) have not been well characterised.Material and methodsLUAD datasets were downloaded from the TCGA database, and the patients were divided into metastasis and non-metastasis groups. The differential expression of lncRNAs (DELs), miRNAs (DEMs), and mRNAs (DEGs) was analysed using the Limma package. Next, interactions between miRNA, lncRNA, and mRNA were predicted by miRcode, miRTarBase, miRDB

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Wen, Xiao, Lin Gao, Tuo Song, and Chaoqun Jiang. "CeNet Omnibus: an R/Shiny application to the construction and analysis of competing endogenous RNA network." BMC Bioinformatics 22, no. 1 (2021). http://dx.doi.org/10.1186/s12859-021-04012-y.

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Abstract Background The competing endogenous RNA (ceRNA) regulation is a newly discovered post-transcriptional regulation mechanism and plays significant roles in physiological and pathological progress. CeRNA networks provide global views to help understand the regulation of ceRNAs. CeRNA networks have been widely used to detect survival biomarkers, select candidate regulators of disease genes, and predict long noncoding RNA functions. However, there is no software platform to provide overall functions from the construction to analysis of ceRNA networks. Results To fill this gap, we introduce

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Han, Pihua, Haiming Yang, Xiang Li, et al. "Identification of a novel cancer stemness-associated ceRNA axis in lung adenocarcinoma via stemness indices analysis." Oncology Research Featuring Preclinical and Clinical Cancer Therapeutics, 2020. http://dx.doi.org/10.3727/096504020x16037124605559.

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To identify a novel cancer stemness-related ceRNA regulatory axis in lung adenocarcinoma (LUAD) via weighted gene coexpression network analysis of a stemness index. The RNA sequencing expression profiles of 513 cancer samples and 60 normal samples were obtained from the TCGA database. Differentially expressed mRNAs (DEmRNAs), lncRNAs (DElncRNAs) and miRNAs (DEmiRNAs) were identified with R software. Functional enrichment analysis was conducted using DAVID 6.8. The ceRNA network was constructed via multiple bioinformatics analyses, and the correlations between possible ceRNAs and prognosis were

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Zhang, Mengying, Xiyun Jin, Junyi Li, et al. "CeRNASeek: an R package for identification and analysis of ceRNA regulation." Briefings in Bioinformatics, May 4, 2020. http://dx.doi.org/10.1093/bib/bbaa048.

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Abstract Competitive endogenous RNA (ceRNA) represents a novel layer of gene regulation that controls both physiological and pathological processes. However, there is still lack of computational tools for quickly identifying ceRNA regulation. To address this problem, we presented an R-package, CeRNASeek, which allows identifying and analyzing ceRNA–ceRNA interactions by integration of multiple-omics data. CeRNASeek integrates six widely used computational methods to identify ceRNA–ceRNA interactions, including two global and four context-specific ceRNA regulation prediction methods. In additio

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Zhu, Dandan, Sifan Wu, Yafang Li, et al. "Ferroptosis-related gene SLC1A5 is a novel prognostic biomarker and correlates with immune infiltrates in stomach adenocarcinoma." Cancer Cell International 22, no. 1 (2022). http://dx.doi.org/10.1186/s12935-022-02544-8.

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Abstract Background Stomach adenocarcinoma (STAD) is associated with high morbidity and mortality rates. Ferroptosis is an iron-dependent form of cell death, which plays an important role in the development of many cancers. Tumor-associated competing endogenous RNAs (ceRNAs) regulate tumorigenesis and development. Our study aimed to construct ceRNA networks and explore the relationship between ferroptosis-related genes in the ceRNA network and immune infiltration in STAD. Methods Based on the interactions among long noncoding RNAs (lncRNAs), microRNAs (miRNAs), and messenger RNAs (mRNAs), a ce

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Xu, Xiaonan, Kaizhen Wang, Olga Vera, et al. "Gain of chromosome 1q perturbs a competitive endogenous RNA network to promote melanoma metastasis." Cancer Research, July 14, 2022. http://dx.doi.org/10.1158/0008-5472.can-22-0283.

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Abstract Somatic copy number alterations (CNA) promote cancer, but the underlying driver genes may not be comprehensively identified if only the functions of the encoded proteins are considered. mRNAs can act as competitive endogenous RNAs (ceRNA) that sponge miRNAs to post-transcriptionally regulate gene expression in a protein coding-independent manner. We investigated the contribution of ceRNAs to the oncogenic effects of CNAs. Chromosome 1q gains promoted melanoma progression and metastasis at least in part through overexpression of three mRNAs with ceRNA activity: CEP170, NUCKS1, and ZC3H

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Xue, Jia, Haoran Chen, Jinqi Lu, et al. "Identification of immunity-related lncRNAs and construction of a ceRNA network of potential prognostic biomarkers in acute myeloid leukemia." Frontiers in Genetics 14 (June 14, 2023). http://dx.doi.org/10.3389/fgene.2023.1203345.

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Objective: Using bioinformatics analyses, this study aimed to identify lncRNAs related to the immune status of acute myeloid leukemia (AML) patients and ascertain the potential impact in immunity-related competing endogenous RNA (ceRNA) networks on AML prognosis.Methods: AML-related RNA-seq FPKM data, AML-related miRNA expression microarray data, and gene sets associated with immunity-related pathways were, respectively, obtained from the TCGA, GEO, and ImmReg databases. An immunity-related ceRNA network was then constructed according to the predicted interactions between AML-related mRNAs, ln

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