Identification of Flap endonuclease 1 as a potential core gene in hepatocellular carcinoma by integrated bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31534853", "kind": "science-record", "revision": 7, "content_hash": "sha256:11da0ea09a565ff6641ed0232b2e8be6a962eb06b5d92878494c5c4453760b97", "created_at": "2026-11-01T15:40:49Z", "updated_at": "2026-11-01T22:00:51Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Flap endonuclease 1 as a potential core gene in hepatocellular carcinoma by integrated bioinformatics analysis.", "doi": "10.7717/peerj.7619", "pmid": "31534853", "authors": ["Chuanfei Li", "Feng Qin", "Hao Hong", "Hui Tang", "Xiaoling Jiang", "Shuangyan Yang", "Zhechuan Mei", "Di Zhou"], "journal": "PeerJ", "year": 2019, "abstract": "Hepatocellular carcinoma (HCC) is a common yet deadly form of malignant cancer. However, the specific mechanisms involved in HCC diagnosis have not yet fully elucidated. Herein, we screened four publically available Gene Expression Omnibus (GEO) expression profiles (GSE14520, GSE29721, GSE45267 and GSE60502), and used them to identify 409 differentially expressed genes (DEGs), including 142 and 267 up- and down-regulated genes, respectively. The DAVID database was used to look for functionally enriched pathways among DEGs, and the STRING database and Cytoscape platform were used to generate a protein-protein interaction (PPI) network for these DEGs. The cytoHubba plug-in was utilized to detect 185 hub genes, and three key clustering modules were constructed with the MCODE plug-in. Gene functional enrichment analyses of these three key clustering modules were further performed, and nine core genes including BIRC5, DLGAP5, DTL, FEN1, KIAA0101, KIF4A, MCM2, MKI67, and RFC4, were identified in the most critical cluster. Subsequently, the hierarchical clustering and expression of core genes in TCGA liver cancer tissues were analyzed using the UCSC Cancer Genomics Browser, and whether elevated core gene expression was linked to a poor prognosis in HCC patients was assessed using the GEPIA database. The PPI of the nine core genes revealed an interaction between FEN1, MCM2, RFC4, and BIRC5. Furthermore, the expression of FEN1 was positively correlated with that of three other core genes in TCGA liver cancer tissues. FEN1 expression in HCC and other tumor types was assessed with the FIREBROWSE and ONCOMINE databases, and results were verified in HCC samples and hepatoma cells. FEN1 levels were also positively correlated with tumor size, distant metastasis and vascular invasion. In conclusion, we identified nine core genes associated with HCC development, offering novel insight into HCC progression. In particular, the aberrantly elevated FEN1 may represent a potential biomarker for HCC diagnosis and treatment.", "claims": [{"id": "claim-method", "statement": "The correlation between FEN1 expression and HCC patient clinicopathological features was investigated via Fisher’s exact test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31534853", "locator": "sections[21] \"Experimental validation\" paragraph 4", "quote": "The correlation between FEN1 expression and HCC patient clinicopathological features was investigated via Fisher’s exact test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The raw measurements are available in Supplemental Files.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31534853", "locator": "sections[25] \"Additional Information and Declarations\" paragraph 6", "quote": "The raw measurements are available in Supplemental Files."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:31534853"], "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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