Identification of prognostic factors for intrahepatic cholangiocarcinoma using long non-coding RNAs-associated ceRNA network.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32694937", "kind": "science-record", "revision": 7, "content_hash": "sha256:42796b382f2b9e883c204d99e8fb89196d1043ac7c8b74b3330ec1e7e1aa1d47", "created_at": "2026-11-01T15:41:06Z", "updated_at": "2026-11-01T22:01:56Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of prognostic factors for intrahepatic cholangiocarcinoma using long non-coding RNAs-associated ceRNA network.", "doi": "10.1186/s12935-020-01388-4", "pmid": "32694937", "authors": ["Zhichen Kang", "Lixin Guo", "Zhuo Zhu", "Rongfeng Qu"], "journal": "Cancer cell international", "year": 2020, "abstract": "BACKGROUND: Accumulating amount of evidence has highlighted the important roles of long non-coding RNAs (lncRNAs) acting as competing endogenous RNAs (ceRNAs) in tumor pathogenesis. However, the roles of long non coding RNAs (lncRNAs) in the lncRNA-related ceRNA network of intrahepatic cholangiocarcinoma (ICC) still remain enigmatic. The current study aims to identify prognostic factors in the lncRNA-related ceRNA network of ICC.\nMETHODS: The transcriptome sequencing data of lncRNAs, messenger RNA (mRNA) and microRNA (miR) were downloaded from the SRA and TCGA databases. Differentially expressed lncRNAs (DElncRNAs), DEmiRs and DEmRNAs were identified and adopted to construct an lncRNA-miR-mRNA ceRNA network. ICC-associated DEmRNAs were adopted to construct the protein-protein interaction (PPI) network. The expression of the top 6 genes in the hub module was validated with mRNA transcriptome sequencing data and ICC-related gene expression dataset GSE45001, followed by GO and KEGG pathway enrichment analysis. The relationship between the hub gene-associated ceRNA network and the overall survival of patients with ICC was predicted by conducting a Kaplan-Meier survival analysis.\nRESULTS: Sixty co-expressed DEmRNAs were identified in the ceRNA network. The top 6 hub genes consisted of downregulated FOS, IGF2, FOXO1 and NTF3, upregulated IGF1R, and insignificantly downregulated HGF in ICC tissues, when compared to that of normal adjacent tissues, followed by the successful construction of lncRNA-miR-hub network consisting of 86 ceRNA modules. MME-AS1 and hsa-miR-182 were associated with overall survival in ICC patients. FOS, IGF1R, IGF2, FOXO1, and NTF3 might target \"TGF-β signaling pathway\", \"the hedgehog signaling pathway\", \"retinol metabolism\", or \"type II diabetes mellitus\" pathways respectively.\nCONCLUSION: These results indicate that FOS, IGF1R, IGF2, FOXO1, and NTF3 were useful prognostic factors in determining the prognosis of patients with ICC.", "claims": [{"id": "claim-method", "statement": "Both the Kaplan–Meier method and the log-rank test were used to determine the relationships between DElncRNAs, DEmiRNAs and DEmRNAs (belonging to the ceRNA network), as well as the overall survival (OS) curve of patients.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32694937", "locator": "sections[8] \"Association analysis of hub gene-related network and prognosis of ICC patients\" paragraph 2", "quote": "Both the Kaplan–Meier method and the log-rank test were used to determine the relationships between DElncRNAs, DEmiRNAs and DEmRNAs (belonging to the ceRNA network), as well as the overall survival (OS) curve of patients."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data sharing not applicable to this article as no datasets were generated or analyzed during the current study.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32694937", "locator": "sections[25] \"Availability of data and materials\" paragraph 2", "quote": "Data sharing not applicable to this article as no datasets were generated or analyzed during the current study."}], "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:32694937"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE26566"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE26566"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32694937", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12935-020-01388-4", "sha256": 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