Bioinformatics Methods Reveal the Biomarkers and the miRNA-mRNA Network in Hepatocellular Carcinoma.

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In this study, datasets including GSE20077 and GSE108724, obtained from the Gene Expression Omnibus (GEO) database, were used for investigating the biomarker and molecular mechanism of HCC. The differentially expressed genes (DEGs) in the datasets were identified, and the targets of the miRNAs were searched in the miRDIP and miRNET databases. Enrichment analysis was performed for delving the molecular mechanism of DEGs, and protein-protein interaction (PPI) networks and miRNA-mRNA networks were used to reveal the hub nodes and the related interaction relationships. Moreover, the expression and diagnostic values of hub nodes were analyzed with the GEPIA2 database. The results showed that 53 upregulated miRNAs and 48 downregulated miRNAs were found in GSE20077, and 55 upregulated miRNAs and 69 downregulated miRNAs were found in GSE108724. Moreover, seven common miRNAs including miR-146b-5p, miR-338-3p, miR-375, miR-502-3p, miR-532-3p, miR-532-5p, and miR-557 were found in the datasets. The targets of the common miRNAs were related with the P53, HIF1, Wnt, and NF-κB pathways. Besides, YWHAZ and CDC42 were identified as the hub nodes and served as the downstream targets of miR-375-3p. The GEPIA2 database showed that YWHAZ and CDC42 were related with the survival rate of the patients. In conclusion, this study suggests that miR-375-3p functions as a tumor suppressor which could inhibit the progression of HCC via targeting YWHAZ and CDC42.", "claims": [{"id": "claim-method", "statement": "The differentially expressed genes (DEGs) in GSE20077 and GSE108724 were obtained with GEO2R analysis of the GEO database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35340237", "locator": "sections[4] \"2.2. Identification of Differentially Expressed Genes\" paragraph 2", "quote": "The differentially expressed genes (DEGs) in GSE20077 and GSE108724 were obtained with GEO2R analysis of the GEO database."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data to support the findings of this study are available on reasonable request from the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35340237", "locator": "sections[17] \"Data Availability\" paragraph 2", "quote": "The data to support the findings of this study are available on reasonable request from the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "GEO2R analysis of GSE20077 and GSE108724 identified 53 upregulated and 48 downregulated miRNAs in GSE20077, 55 upregulated and 69 downregulated miRNAs in GSE108724, and seven common miRNAs.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35340237", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The results showed that 53 upregulated miRNAs and 48 downregulated miRNAs were found in GSE20077, and 55 upregulated miRNAs and 69 downregulated miRNAs were found in GSE108724."}, {"asset": "source:pmid:35340237", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Moreover, seven common miRNAs including miR-146b-5p, miR-338-3p, miR-375, miR-502-3p, miR-532-3p, miR-532-5p, and miR-557 were found in the datasets."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "GEO2R analysis of GSE20077 and GSE108724 identified 53 upregulated and 48 downregulated miRNAs in GSE20077, 55 upregulated and 69 downregulated miRNAs in GSE108724, and seven common miRNAs.", "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:35340237"], "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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