Construct a ceRNA regulatory network to explore potential pathogenesis and therapy options of human hepatocellular carcinoma
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1014754 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The human circRNA profiles of Hepatocellular carcinoma are rarely reported. Surgically removed human HCC tissues and matched normal liver tissues (5cm away from tumor) were collected to make an Agilent microarray.
2023-12-20 | GSE242797 | GEO
Project description:To explore the lncRNAs and mRNA expression profiles in CHB and asymptomatic HBsAg carriers (ASC) and construct mRNA-lncRNA co-expression profile and ceRNA networks to identify the potential targets of diagnosis and treatment in CHB.
2019-08-27 | GSE136343 | GEO
Project description:Clear cell renal cell carcinoma (ccRCC) is the most representative subtype of renal cancer. CircRNA acts as a kind of ceRNA to play a role in regulating microRNA (miRNA) in many cancers. However, the potential pathogenesis role of the regulatory network among circRNA/miRNA/mRNA is not clear and has not been fully explored. CircRNA expression profile data were obtained from GEO datasets, and the differentially expressed circRNAs (DECs) were identified through utilizing R package (Limma) firstly. Secondly, miRNAs that were regulated by these circRNAs were predicted by using Cancer-specific circRNA database and Circular RNA Interactome. Thirdly, some related genes were identified by intersecting targeted genes, which was predicted by a web tool (miRWalk) and differentially expressed genes, which was obtained from TCGA datasets. Function enrichment was analyzed, and a PPI network was constructed by Cytoscape software and DAVID web set. Subsequently, ten hub-genes were screened from the network, and the overall survival time in patients of ccRCC with abnormal expression of these hub-genes were completed by GEPIA web set. In the last, a circRNA/miRNA/mRNA regulatory network was constructed, and potential compounds and drug which may have the function of anti ccRCC were forecasted by taking advantage of CMap and PharmGKB datasets. Six DECs (hsa_circ_0029340, hsa_circ_0039238, hsa_circ_0031594, hsa_circ_0084927, hsa_circ_0035442, hsa_circ_0025135) were obtained and six miRNAs (miR-1205, miR-657, miR-587, miR-637, miR-1278, miR-548p) which are regulated by three circRNAs (hsa_circ_0084927, hsa_circ_0035442, hsa_circ_0025135) were also predicted. Then 497 overlapped genes regulated by these six miRNAs above had been predicted, and function enrichment analysis revealed these genes are mainly linked with some regulation functions of cancers. Ten hub-genes (PTGER3, ADCY2, APLN, CXCL5, GRM4, MCHR1, NPY5R, CXCR4, ACKR3, MTNR1B) have been screened from a PPI network. PTGER3, ADCY2, CXCL5, GRM4 and APLN were identified to have a significant effect on the overall survival time of patients with ccRCC. Furthermore, one compound (josamycin) and four kinds of drugs (capecitabine, hmg-coa reductase inhibitors, ace Inhibitors and bevacizumab) were confirmed as potential therapeutic options for ccRCC by CMap analysis and pharmacogenomics analysis. This study implies the potential pathogenesis of the regulatory network among circRNA/miRNA/mRNA and provides some potential therapeutic options for ccRCC.
| S-EPMC7423896 | biostudies-literature
Project description:Expression changes of competitive endogenous RNAs (ceRNAs) have been proposed to influence microRNA (miRNA) activity and thereby regulate other transcripts that contain miRNA binding sites. Here, we find that although miRNA levels define the extent of repression, they do not affect the magnitude of the ceRNA expression change required to observe derepression. Canonical 6-nt sites, which typically mediate modest repression, can nonetheless compete for miRNA binding, with potency ~20% of that observed for canonical 8-nt sites. Sites with extensive additional complementarity can be even more potent, but this occurs predominantly through miRNA degradation rather than competition. Cooperative binding of closely spaced sites for different miRNAs can also increase potency. These results provide quantitative insights into the stoichiometric relationship between miRNA and target abundance, target-site spacing and affinity requirements for ceRNA-mediated gene regulation and specify the unusual circumstances in which ceRNA-mediated gene regulation might be observed. Sixty-four mRNA profiles were generated of 1) primary hepatocytes of mice expressing variable levels of a recombinant Adenovirus expressing the transcript of AldolaseA (Ad-AldoA), containing sites matching miR-122, let-7, miR-192, miR-194 or a mutated site (no site) or 2) embryonic stem (ES) cells that were transfected with a Tet-inducible dual-color reporter construct expressing enhanced yellow fluorescent protein (eYFP) and mCherry that contains zero (0s) or three (3s) 8 nt miRNA seed matches for miR-293 or miR-92 in the 3� UTR. ES cells were sorted with a FACSAria IIIu flow cytometer into three bins based on their eYFP fluorescence intensity. All samples were sequenced in duplicates by an Illumina HiSeq 2500. Library preparation and sequencing were performed by Fasteris SA (Switzerland) or by the Functional Genomics Centre Zürich (FGCZ). Three small RNA profiles or either primary hepatocytes or embryonic stem cells were also generated by Solexa sequencing.
2016-10-27 | E-GEOD-76288 | biostudies-arrayexpress
Project description:Alzheimer’s disease (AD) is a progressive neurodegenerative disorder, and the molecular mechanisms of AD remain unclear. Accumulating evidence indicates the involvement of non-coding RNAs in AD pathogenesis. Here, we applied RNA-seq to explore the expression changes of circRNA, miRNA, and mRNA simultaneously, and investigate competing endogenous RNA (ceRNA) networks in hippocampus of 4-month APP/PS1 and wild-type mice.
2022-07-27 | GSE166393 | GEO
Project description:Purpose:The purpose of this study is to investigate the potential mechanisms that triggering the onset of constrictive pericarditis and to screen hub genes that exert impact on pathogenesis of patients with constrictive pericarditis. Methods: We screened differentially expressed genes with the data obtained from RNA-seq on CP samples and matched normal samples. Functional annotation analysis and protein-protein interaction (PPI) network were performed to investigate the potential key pathways and genes that play significant roles in CP. Furthermore, the ceRNA network was established and the Gene Set Enrichment Analysis (GSEA) was executed to dig key circRNAs. Results: Following the identification of differentially expressed genes, functional annotation analysis was conducted, suggesting that differentially expressed mRNAs (DEMs) were mainly involved in inflammatory response related pathways. The top 11 genes with the highest degree were extracted from PPI network. A total of 377 predicted regulatory relationships among the differentially expressed genes were found and the ceRNA network was established. Finally, GSEA was conducted on the circRNAs and the key biological pathways were identified. Conclusion: Our study is the pioneering research to analyze the pathogenesis of CP with integrated informatics and we have identified several hub genes, which reveals that the generation of CP is closely related to inflammation and fibrosis.
2020-05-19 | GSE122904 | GEO
Project description:Purpose:The purpose of this study is to investigate the potential mechanisms that triggering the onset of constrictive pericarditis and to screen hub genes that exert impact on pathogenesis of patients with constrictive pericarditis. Methods: We screened differentially expressed genes with the data obtained from RNA-seq on CP samples and matched normal samples. Functional annotation analysis and protein-protein interaction (PPI) network were performed to investigate the potential key pathways and genes that play significant roles in CP. Furthermore, the ceRNA network was established and the Gene Set Enrichment Analysis (GSEA) was executed to dig key circRNAs. Results: Following the identification of differentially expressed genes, functional annotation analysis was conducted, suggesting that differentially expressed mRNAs (DEMs) were mainly involved in inflammatory response related pathways. The top 11 genes with the highest degree were extracted from PPI network. A total of 377 predicted regulatory relationships among the differentially expressed genes were found and the ceRNA network was established. Finally, GSEA was conducted on the circRNAs and the key biological pathways were identified. Conclusion: Our study is the pioneering research to analyze the pathogenesis of CP with integrated informatics and we have identified several hub genes, which reveals that the generation of CP is closely related to inflammation and fibrosis.
2020-05-19 | GSE122903 | GEO