Identification of potentially functional circular RNAs hsa_circ_0070934 and hsa_circ_0004315 as prognostic factors of hepatocellular carcinoma by integrated bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35322101", "kind": "science-record", "revision": 5, "content_hash": "sha256:41ff5b9a6a2b760d1874401a215f67d50fbf4e2bb2f5492fa2d40c534f71d11a", "created_at": "2026-11-01T18:14:07Z", "updated_at": "2026-11-01T22:48:43Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of potentially functional circular RNAs hsa_circ_0070934 and hsa_circ_0004315 as prognostic factors of hepatocellular carcinoma by integrated bioinformatics analysis.", "doi": "10.1038/s41598-022-08867-w", "pmid": "35322101", "authors": ["Pejman Morovat", "Saman Morovat", "Arash M Ashrafi", "Shahram Teimourian"], "journal": "Scientific reports", "year": 2022, "abstract": "Hepatocellular carcinoma (HCC) is one of the most prevalent cancers worldwide, which has a high mortality rate and poor treatment outcomes with yet unknown molecular basis. It seems that gene expression plays a pivotal role in the pathogenesis of the disease. Circular RNAs (circRNAs) can interact with microRNAs (miRNAs) to regulate gene expression in various malignancies by acting as competitive endogenous RNAs (ceRNAs). However, the potential pathogenesis roles of the ceRNA network among circRNA/miRNA/mRNA in HCC are unclear. In this study, first, the HCC circRNA expression data were obtained from three Gene Expression Omnibus microarray datasets (GSE164803, GSE94508, GSE97332), and the differentially expressed circRNAs (DECs) were identified using R limma package. Also, the liver hepatocellular carcinoma (LIHC) miRNA and mRNA sequence data were retrieved from TCGA and differentially expressed miRNAs (DEMIs) and mRNAs (DEGs) were determined using the R DESeq2 package. Second, CSCD website was used to uncover the binding sites of miRNAs on DECs. The DECs' potential target miRNAs were revealed by conducting an intersection between predicted miRNAs from CSCD and downregulated DEMIs. Third, candidate genes were uncovered by intersecting targeted genes predicted by miRWalk and targetscan online tools with upregulated DEGs. The ceRNA network was then built using the Cytoscape software. The functional enrichment and the overall survival time of these potential targeted genes were analyzed, and a PPI network was constructed in the STRING database. Network visualization was performed by Cytoscape, and ten hub genes were detected using the CytoHubba plugin tool. Four DECs (hsa_circ_0000520, hsa_circ_0008616, hsa_circ_0070934, hsa_circ_0004315) were obtained and six miRNAs (hsa-miR-542-5p, hsa-miR-326, hsa-miR-511-5p, hsa-miR-195-5p, hsa-miR-214-3p, and hsa-miR-424-5p) which are regulated by the above DECs were identified. Then 543 overlapped genes regulated by six miRNAs mentioned above were predicted. Functional enrichment analysis showed that these genes are mostly associated with regulatory pathways in cancer. Ten hub genes (TTK, AURKB, KIF20A, KIF23, CEP55, CDC6, DTL, NCAPG, CENPF, PLK4) have been screened from the PPI network of the 204 survival-related genes. KIF20A, NCAPG, TTK, PLK4, and CDC6 were selected for the highest significance p-values. At the end, a circRNA-miRNA-mRNA regulatory axis was established for five final selected hub genes. This study implies the potential pathogenesis of the obtained network and proposes that the two DECs (has_circ_0070934 and has_circ_0004315) may be important prognostic markers for HCC.", "claims": [{"id": "claim-method", "statement": "The R limma package (V 3.48.3)21 based on the Bioconductor package was applied to screen DECs microarray datasets with the cutoff criteria of |log2FoldChange|≥ 1.5 and adj. p-value < 0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35322101", "locator": "sections[3] \"Microarray data collection and identification of differentially expressed circRNAs (DECs)\" paragraph 3", "quote": "The R limma package (V 3.48.3)21 based on the Bioconductor package was applied to screen DECs microarray datasets with the cutoff criteria of |log2FoldChange|≥ 1.5 and adj. p-value < 0.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The authors declare that the data supporting the findings of this study are addressed within the article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35322101", "locator": "sections[23] \"Data availability\" paragraph 2", "quote": "The authors declare that the data supporting the findings of this study are addressed within the article."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Four differentially expressed circRNAs and six regulatory miRNAs were identified, leading to a circRNA–miRNA–mRNA regulatory network and five final hub genes in hepatocellular carcinoma.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35322101", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Four DECs (hsa_circ_0000520, hsa_circ_0008616, hsa_circ_0070934, hsa_circ_0004315) were obtained and six miRNAs (hsa-miR-542-5p, hsa-miR-326, hsa-miR-511-5p, hsa-miR-195-5p, hsa-miR-214-3p, and hsa-miR-424-5p) which are regulated by the above DECs were identified."}, {"asset": "source:pmid:35322101", "locator": "sections[14] \"Prediction and analysis of miRNA-mRNA pairs and construction of ceRNA network\" paragraph 4", "quote": "Finally, there were 300 interactions in the ceRNA network, including four DECs, six FImiRNAs, and 543 FImRNAs (Fig. 5)."}, {"asset": "source:pmid:35322101", "locator": "sections[17] \"Discussion\" paragraph 16", "quote": "The top five hub genes based on the most significant p-value among these ten hub genes that considerably affect overall survival are KIF20A, NCAPG, TTK, PLK4, and CDC6."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Four differentially expressed circRNAs and six regulatory miRNAs were identified, leading to a circRNA–miRNA–mRNA regulatory network and five final hub genes in hepatocellular carcinoma.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:35322101"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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