scholarly journals Integrated analysis of lncRNA-miRNA-mRNA ceRNA network and the potential prognosis indicators in sarcomas

2020 ◽  
Author(s):  
Ling Zhang ◽  
Lu Gao ◽  
Yu Zhao ◽  
Xuelei Ma
Keyword(s):  
Survival Analysis ◽  
Protein Interactions ◽  
Sequence Data ◽  
Gene Prediction ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Integrated Analysis ◽  
Pathway Enrichment Analysis ◽  
Tissue Samples ◽  
Cerna Network

Abstract The ceRNA network has been demonstrated to play crucial roles in multiple biological processes and the development of neoplasms, which have the potential to become diagnostic and prognosis markers and therapeutic targets. In this work, we comparing the expression profiles between sarcoma identified differentially expressed genes (DEGs), lncRNAs (DELs) and miRNAs (DEMs) in sarcomas and normal tissue samples in GEO datasets. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were applied to investigate the major functions of the overlapping DEGs. Then, lncRNA-miRNA interactions and miRNA-mRNA interactions were predicted, and a ceRNA regulatory network was constructed. In addition, the mRNAs included in ceRNA network were used to construct the protein-protein interactions network, and the survival analysis of sarcomas was performed according to the biomarkers included in the ceRNA network. According to the RNA sequence data from GEO dataset, 1296 DEGs were identified in sarcoma samples by combining the GO and Pathway enrichment analysis, 338 DELs were discovered after re-annotating the probes, and 36 DEGs were ascertained through intersecting two different expression miRNAs sets. Further, 448 miRNA-mRNA interactions and 454 miRNA-lncRNA interactions were obtained through target gene prediction, and then, we constructed a lncRNA-miRNA-mRNA ceRNA network containing 9 miRNAs, 69 lncRNAs and 113 mRNAs. PPI network showed that the hub up-regulated nodes include IGF1, PRKCB and GNAI3, and the hub down-regulated nodes include AR, CYCS and PPP1CB. Survival analysis revealed that the expression levels of 12 RNAs involved in the ceRNA network were associated with overall survival of sarcoma patients. Our study showed that the ceRNA network in sarcomas based on that lncRNA could serve as ceRNA and discovered the potential indicators for prognosis of sarcoma patients.

scholarly journals Integrated analysis of lncRNA-miRNA-mRNA ceRNA network and the potential prognosis indicators in sarcomas

2021 ◽  
Author(s):  
Lu Gao ◽  
Yu Zhao ◽  
Xuelei Ma ◽  
Ling Zhang
Keyword(s):  
Survival Analysis ◽  
Kegg Pathway ◽  
Gene Prediction ◽  
Expression Profiles ◽  
Gene Expression Omnibus ◽  
Integrated Analysis ◽  
Ppi Network ◽  
Tissue Samples ◽  
Pathway Enrichment ◽  
Cerna Network

Abstract Background: Competitive endogenous RNA (ceRNA) has revealed a new mechanism of interaction between RNAs and been demonstrated to play crucial roles in multiple biological processes and in the development of neoplasms that potentially serve as diagnostic and prognosis markers as well as therapeutic targets.Methods：In this work, we identified differentially expressed mRNAs (DEGs), lncRNAs (DELs) and miRNAs (DEMs) in sarcoma by comparing the genes expression profiles between sarcoma samples and normal tissue samples in Gene Expression Omnibus (GEO) datasets. Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analyses were applied to investigate the primary functions of the overlapped DEGs. Then, lncRNA-miRNA and miRNA-mRNA interactions were predicted, and the ceRNA regulatory network was constructed in Cytoscape. In addition, the protein-protein interaction (PPI) network was constructed and survival analysis was performed.Results: A total of 1296 DEGs were identified in sarcoma samples by combining the GO and KEGG pathway enrichment analyses, 338 DELs were discovered after the probes were reannotated, and 36 DEMs were ascertained through intersecting two different expression miRNAs sets. Further, through target gene prediction, a lncRNA-miRNA-mRNA ceRNA network that contained 113 mRNAs, 69 lncRNAs and 29 miRNAs was constructed. The PPI network identified the six most significant hub proteins. Survival analysis revealed that seven mRNAs, four miRNAs and one lncRNA were associated with overall survival of sarcoma patients.Conclusions: Overall, we constructed a ceRNA network in sarcomas, which likely provides insights for further research on the molecular mechanism and potential prognosis biomarkers.

scholarly journals Integrated analysis of lncRNA-miRNA-mRNA ceRNA network and the potential prognosis indicators in sarcomas

2020 ◽  
Author(s):  
Lu Gao ◽  
Yu Zhao ◽  
Xuelei Ma ◽  
Ling Zhang
Keyword(s):  
Survival Analysis ◽  
Kegg Pathway ◽  
Gene Prediction ◽  
Expression Profiles ◽  
Gene Expression Omnibus ◽  
Integrated Analysis ◽  
Ppi Network ◽  
Tissue Samples ◽  
Pathway Enrichment ◽  
Cerna Network

Abstract Background: Competitive endogenous RNA (ceRNA) has been demonstrated to play crucial roles in multiple biological processes and in the development of neoplasms that potentially serve as diagnostic and prognosis markers as well as therapeutic targets.Methods: In this work, we identified differentially expressed mRNAs (DEGs), lncRNAs (DELs) and miRNAs (DEMs) in sarcoma by comparing the genes expression profiles between sarcoma samples and normal tissue samples in Gene Expression Omnibus (GEO) datasets. Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analyses were applied to investigate the primary functions of the overlapped DEGs. Then, lncRNA-miRNA and miRNA-mRNA interactions were predicted, and the ceRNA regulatory network was constructed in Cytoscape. In addition, the protein-protein interaction (PPI) network was constructed and survival analysis was performed.Results: A total of 1296 DEGs were identified in sarcoma samples by combining the GO and KEGG pathway enrichment analyses, 338 DELs were discovered after the probes were reannotated, and 36 DEMs were ascertained through intersecting two different expression miRNAs sets. Further, through target gene prediction, a lncRNA-miRNA-mRNA ceRNA network that contained 113 mRNAs, 69 lncRNAs and 29 miRNAs was constructed. The PPI network identified the six most significant hub proteins. Survival analysis revealed that seven mRNAs, four miRNAs and one lncRNA were associated with overall survival of sarcoma patients.Conclusions: Overall, we constructed a ceRNA network in sarcomas, which likely provides insights for further research on the molecular mechanism and potential prognosis biomarkers.

scholarly journals Integrated analysis of lncRNA–miRNA–mRNA ceRNA network and the potential prognosis indicators in sarcomas

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Lu Gao ◽  
Yu Zhao ◽  
Xuelei Ma ◽  
Ling Zhang
Keyword(s):  
Gene Expression ◽  
Survival Analysis ◽  
Gene Prediction ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Gene Expression Omnibus ◽  
Integrated Analysis ◽  
Ppi Network ◽  
Protein Protein Interaction ◽  
Cerna Network

Abstract Background Competitive endogenous RNA (ceRNA) networks have revealed a new mechanism of interaction between RNAs, and play crucial roles in multiple biological processes and development of neoplasms. They might serve as diagnostic and prognosis markers as well as therapeutic targets. Methods In this work, we identified differentially expressed mRNAs (DEGs), lncRNAs (DELs) and miRNAs (DEMs) in sarcomas by comparing the gene expression profiles between sarcoma and normal muscle samples in Gene Expression Omnibus (GEO) datasets. Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analyses were applied to investigate the primary functions of the overlapped DEGs. Then, lncRNA-miRNA and miRNA-mRNA interactions were predicted, and the ceRNA regulatory network was constructed using Cytoscape software. In addition, the protein–protein interaction (PPI) network and survival analysis were performed. Results A total of 1296 DEGs were identified in sarcoma samples by combining the GO and KEGG enrichment analyses, 338 DELs were discovered after the probes were reannotated, and 36 DEMs were ascertained through intersecting two different expression miRNAs sets. Further, through target gene prediction, a lncRNA–miRNA–mRNA ceRNA network that contained 113 mRNAs, 69 lncRNAs and 29 miRNAs was constructed. The PPI network identified the six most significant hub proteins. Survival analysis revealed that seven mRNAs, four miRNAs and one lncRNA were associated with overall survival of sarcoma patients. Conclusions Overall, we constructed a ceRNA network in sarcomas, which might provide insights for further research on the molecular mechanism and potential prognosis biomarkers.

scholarly journals Perturbed functional networks in Alzheimer’s Disease reveal opposing roles for TGIF and EGR3

2018 ◽  
Author(s):  
Saranya Canchi ◽  
Balaji Raao ◽  
Deborah Masliah ◽  
Sara Brin Rosenthal ◽  
Roman Sasik ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Cell Cycle ◽  
Alzheimer's Disease ◽  
Brain Tissue ◽  
Protein Interactions ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Large Set ◽  
Tissue Samples ◽  
Vesicle Cycle

AbstractWhile Alzheimer’s disease (AD) is the most prevalent cause of dementia, complex combinations of the underlying pathologies have led to evolved concepts in clinical and neuropathological criteria in the past decade. Pathological AD can be decomposed into subsets of individuals with significantly different antemortem cognitive decline rates. Using transcriptome as a proxy for functional state, we preselected 414 expression profiles of clinically and neuropathologically confirmed AD subjects and age matched non-demented controls sampled from a large community based neuropathological study. By combining brain tissue specific protein interactome with gene network, we identify functionally distinct composite clusters of genes which reveal extensive changes in expression levels in AD. The average global expression for clusters corresponding to synaptic transmission, metabolism, cell cycle, survival and immune response were downregulated while the upregulated cluster had a large set of uncharacterized pathways and processes that may constitute an AD specific phenotypic signature. We identified four master regulators across all clusters of differentially expressed genes by enrichment analysis includingTGIF1andEGR3.These transcription factors have previously not been associated with AD and were validated in brain tissue samples from an independent AD cohort. We identifyTGIF1,a transcriptional repressor as being neuroprotective in AD by activating co-repressors regulating genes critical for DNA repair, maintaining homeostasis and arresting cell cycle. In addition, we show that loss ofEGR3regulation, mediates synaptic deficits by targeting the synaptic vesicle cycle. Collectively, our results highlight the utility of integrating protein interactions with gene perturbations to generate a comprehensive framework for characterizing the alterations in molecular network as applied to AD.

scholarly journals Bioinformatics analysis of potential core genes for glioblastoma

2020 ◽  
Vol 40 (7) ◽  
Author(s):  
Yu Zhang ◽  
Xin Yang ◽  
Xiao-Lin Zhu ◽  
Jia-Qi Hao ◽  
Hao Bai ◽  
...  
Keyword(s):  
Survival Analysis ◽  
Protein Interactions ◽  
Poor Prognosis ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Pathway Enrichment Analysis ◽  
Normal Brain ◽  
Hub Genes ◽  
Potential Core ◽  
Core Genes

Abstract Background: Glioblastoma (GBM) has a high degree of malignancy, aggressiveness and recurrence rate. However, there are limited options available for the treatment of GBM, and they often result in poor prognosis and unsatisfactory outcomes. Materials and methods: In order to identify potential core genes in GBM that may provide new therapeutic insights, we analyzed three gene chips (GSE2223, GSE4290 and GSE50161) screened from the GEO database. Differentially expressed genes (DEG) from the tissues of GBM and normal brain were screened using GEO2R. To determine the functional annotation and pathway of DEG, Gene Ontology (GO) and KEGG pathway enrichment analysis were conducted using DAVID database. Protein interactions of DEG were visualized using PPI network on Cytoscape software. Next, 10 Hub nodes were screened from the differentially expressed network using MCC algorithm on CytoHubba software and subsequently identified as Hub genes. Finally, the relationship between Hub genes and the prognosis of GBM patients was described using GEPIA2 survival analysis web tool. Results: A total of 37 up-regulated and 187 down-regulated genes were identified through microarray analysis. Amongst the 10 Hub genes selected, SV2B appeared to be the only gene associated with poor prognosis in glioblastoma based on the survival analysis. Conclusion: Our study suggests that high expression of SV2B is associated with poor prognosis in GBM patients. Whether SV2B can be used as a new therapeutic target for GBM requires further validation.

scholarly journals Integrated Analysis of lncRNA-miRNA-mRNA ceRNA Network in Human Diarrhea Irritable Bowel Syndrome

2021 ◽  
Author(s):  
Jun-wei LIANG ◽  
Wen-jun BAI ◽  
Xiao-yan WANG ◽  
Li-li CHI
Keyword(s):  
Irritable Bowel Syndrome ◽  
Molecular Mechanisms ◽  
Enrichment Analysis ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Down Regulation ◽  
Tissue Samples ◽  
Cerna Network ◽  
Irritable Bowel

Abstract Background:Many studies on long chain non-coding RNAs (lncRNAs) are published in recent years. But the roles of lncRNAs in diarrhea irritable bowel syndrome (IBS-D) are still unclear and should be further examined. The present work focused on determining the molecular mechanisms underlying lncRNAs regulation in IBS-D on the basis of the lncRNA-miRNA-mRNA competing endogenous RNA (ceRNA) network.Methods:This study collected the mRNAs (GSE36701) expression data within human tissue samples with IBS-D group and normal group based on Gene Expression Omnibus (GEO) database and collected the differentially expressed lncRNAs (DELs) and differentially expressed miRNAs (DEmiRs) based on PubMed.Functional enrichment analysis of DEGs was performed on the DAVID database. Then the interaction network was constructed and visualized using STRING database and Cytoscape.Results: This study identified 3192 DEmRNAs (1437 with up-regulation and 1755 with down-regulation),29 DEmiRs (18 upregulated and 11 downregulated)and 2 DELs(one upregulated and one downregulated) between IBS-D and control samples.Furthermore,we constructed a lncRNA-miRNA-mRNA network through two DELs (lncRNA TUG1 with up-regulation and lncRNA H19 with down-regulation), four DemiRs (hsa-miR-148a-3p,hsa-miR-342-3p,hsa-miR-149-5p with up-regulation and hsa-miR-219a-5p with down-regulation)and 24 DEGs (4 with up-regulation and 20 with down-regulation) with 42 axes. Simultaneously, we conducted functional enrichment and pathway analyses on genes within the as-constructed ceRNA network. According to our PPI/ceRNA network and functional enrichment analysis results, two critical genes were found (BCL2L11 and QKI). Conclusion:In conclusion, the ceRNA interaction axis we identified is a potentially critical target for treating IBS-D.BCL2L11 axis(LncH19-hsa-miR-148a-3p-BCL2L11) may via interaction with PI3K/AKT pathways in IBS-D.Our results shed more lights on the possible pathogenic mechanism in IBS-D using a lncRNA-associated ceRNA network.

scholarly journals Integrated Analysis of Circular RNA-Associated ceRNA Network Reveals Potential circRNA Biomarkers in Human Breast Cancer

2021 ◽  
Vol 2021 ◽  
pp. 1-16
Author(s):  
Han Sheng ◽  
Huan Pan ◽  
Ming Yao ◽  
Longsheng Xu ◽  
Jianju Lu ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Survival Analysis ◽  
Correlation Analysis ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Circular Rna ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Cerna Network

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 expressed mRNAs (DEmRNAs), differentially expressed miRNAs (DEmiRNAs), and differentially expressed circRNAs (DEcircRNAs) were identified, and a competitive endogenous RNA (ceRNA) regulatory network was constructed based on circRNA–miRNA pairs and miRNA–mRNA pairs. Gene ontology and pathway enrichment analyses were performed on mRNAs regulated by circRNAs in ceRNA networks. Survival analysis and correlation analysis of all mRNAs and miRNAs in the ceRNA network were performed. A total of 72 DEcircRNAs, 158 DEmiRNAs, and 2762 DE mRNAs were identified. The constructed ceRNA network contains 60 circRNA–miRNA pairs and 140 miRNA–mRNA pairs, including 40 circRNAs, 30 miRNAs, and 100 mRNAs. Functional enrichment indicated that DEmRNAs regulated by DEcircRNAs in ceRNA networks were significantly enriched in the PI3K-Akt signaling pathway, microRNAs in cancer, and proteoglycans in cancer. Survival analysis and correlation analysis of all mRNAs and miRNAs in the ceRNA network showed that 13 mRNAs and 6 miRNAs were significantly associated with overall survival, and 48 miRNA–mRNA interaction pairs had a significant negative correlation. A PPI network was established, and 21 hub genes were determined from the network. This study provides an effective bioinformatics basis for further understanding of the molecular mechanisms and predictions of breast cancer. A better understanding of the circRNA-related ceRNA network in BRCA will help identify potential biomarkers for diagnosis and prognosis.

scholarly journals Integrated analysis of lncRNA-miRNA-mRNA ceRNA network in human aortic dissection

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Hao Zhang ◽  
Ce Bian ◽  
Simei Tu ◽  
Fanxing Yin ◽  
Panpan Guo ◽  
...  
Keyword(s):  
Aortic Dissection ◽  
Molecular Mechanisms ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Down Regulation ◽  
Tissue Samples ◽  
Cerna Network

Abstract Background Many studies on long chain non-coding RNAs (lncRNAs) are published in recent years. But the roles of lncRNAs in aortic dissection (AD) are still unclear and should be further examined. The present work focused on determining the molecular mechanisms underlying lncRNAs regulation in aortic dissection on the basis of the lncRNA-miRNA-mRNA competing endogenous RNA (ceRNA) network. Methods This study collected the lncRNAs (GSE52093), mRNAs (GSE52093) and miRNAs (GSE92427) expression data within human tissue samples with aortic dissection group and normal group based on Gene Expression Omnibus (GEO) database. Results This study identified three differentially expressed lncRNAs (DELs), 19 differentially expressed miRNAs (DEmiRs) and 1046 differentially expressed mRNAs (DEGs) identified regarding aortic dissection. Furthermore, we constructed a lncRNA-miRNA-mRNA network through three lncRNAs (including two with up-regulation and one with down-regulation), five miRNAs (five with up-regulation), as well as 211 mRNAs (including 103 with up-regulation and 108 with down-regulation). Simultaneously, we conducted functional enrichment and pathway analyses on genes within the as-constructed ceRNA network. According to our PPI/ceRNA network and functional enrichment analysis results, four critical genes were found (E2F2, IGF1R, BDNF and PPP2R1B). In addition, E2F2 level was possibly modulated via lncRNA FAM87A-hsa-miR-31-5p/hsa-miR-7-5p or lncRNA C9orf106-hsa-miR-7-5p. The expression of IGF1R may be regulated by lncRNA FAM87A-hsa-miR-16-5p/hsa-miR-7-5p or lncRNA C9orf106-hsa-miR-7-5p. Conclusion In conclusion, the ceRNA interaction axis we identified is a potentially critical target for treating AD. Our results shed more lights on the possible pathogenic mechanism in AD using a lncRNA-associated ceRNA network.

scholarly journals Identification of candidate genes and proteins in aging skeletal muscle (sarcopenia) using gene expression and structural analysis

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5239 ◽  
Author(s):  
Gita Shafiee ◽  
Yazdan Asgari ◽  
Akbar Soltani ◽  
Bagher Larijani ◽  
Ramin Heshmat
Keyword(s):  
Gene Expression ◽  
Skeletal Muscle ◽  
Ribosome Biogenesis ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Lipid Storage ◽  
Integrated Analysis ◽  
Pathway Enrichment Analysis ◽  
Ppi Network ◽  
Men And Women

Sarcopenia is an age-related disease characterized by the loss of muscle mass and muscle function. A proper understanding of its pathogenesis and mechanisms may lead to new strategies for diagnosis and treatment of the disease. This study aims to discover the underlying genes, proteins, and pathways associated with sarcopenia in both genders. Integrated analysis of microarray datasets has been performed to identify differentially expressed genes (DEGs) between old and young skeletal muscles. Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were then performed to uncover the functions of the DEGs. Moreover, a protein–protein interaction (PPI) network was constructed based on the DEGs. We have identified 41,715 DEGs, including 19 downregulated and 41,696 upregulated ones, in men. Among women, 3,015 DEGs have been found, with 2,874 of them being upregulated and 141 downregulated genes. Among the top up-regulated and downregulated genes, the ribosome biogenesis genes and genes involved in lipid storage may be closely related to aging muscles in men and women respectively. Also, the DEGs were enriched in the pathways including those of ribosome and Peroxisome proliferator-activated receptor (PPAR) in men and women, respectively. In the PPI network, Neurotrophic Receptor Tyrosine Kinase 1 (NTRK1), Cullin 3 (CUL3) and P53 have been identified as significant hub proteins in both genders. Using the integrated analysis of multiple gene expression profiles, we propose that the ribosome biogenesis genes and those involved in lipid storage would be promising markers for sarcopenia in men and women, respectively. In the reconstructed PPI network, neurotrophic factors expressed in skeletal muscle are essential for motoneuron survival and muscle fiber innervation during development. Cullin E3 ubiquitin ligase (Cul3) is an important component of the ubiquitin–proteasome system—it regulates the proteolysis. P53 is recognized as a central regulator of the cell cycle and apoptosis. These proteins, which have been identified as the most significant hubs, may be involved in aging muscle and sarcopenia.

scholarly journals Identification of pivotal lncRNAs in papillary thyroid cancer using lncRNA–mRNA–miRNA ceRNA network analysis

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7441 ◽  
Author(s):  
Weiwei Liang ◽  
Fangfang Sun
Keyword(s):  
Gene Expression ◽  
Thyroid Cancer ◽  
Network Analysis ◽  
Papillary Thyroid Cancer ◽  
Enrichment Analysis ◽  
Integrated Analysis ◽  
Pathway Enrichment Analysis ◽  
Papillary Thyroid ◽  
Cerna Network ◽  
Go Terms

Background To identify pivotal lncRNAs in papillary thyroid cancer (PTC) using lncRNA–mRNA–miRNA ceRNA network analysis. Methods We obtained gene expression profiles from the gene expression omnibus database. Cancer specific lncRNA, cancer specific miRNA and cancer specific mRNA were identified. An integrated analysis was conducted to detect potential lncRNA–miRNA–mRNA ceRNA in regulating disease transformation. The lncRNA regulated gene ontology (GO) terms and regulated pathways were performed by function analysis. Survival analysis was performed for the pivotal lncRNAs. Results A total of four lncRNAs, 15 miRNAs and 375 mRNAs are identified as the key mediators in the pathophysiological processes of PTC. GO annotation enrichment analysis showed the most relevant GO terms are signal transduction, integral component of membrane and calcium ion binding. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed different changed genes mainly enriched in pathways in cancer, PI3K-Akt signaling pathway and focal adhesion. Among four lncRNAs, only SLC26A4-AS1 was significantly associated with PTC patient disease free survival. Conclusion This study has constructed lncRNA–mRNA–miRNA ceRNA networks in PTC. The study provides a set of pivotal lncRNAs for future investigation into the molecular mechanisms.

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