Bioinformatics Analysis Identifies the Estrogen Receptor 1 (ESR1) Gene and hsa-miR-26a-5p as Potential Prognostic Biomarkers in Patients with Intrahepatic Cholangiocarcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32435051", "kind": "science-record", "revision": 8, "content_hash": "sha256:e66ebcb946da5d0bc20a4ed923040c864aee20b19eee9f60444d5efdfff1d6ec", "created_at": "2026-11-01T15:41:02Z", "updated_at": "2026-11-01T22:44:53Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics Analysis Identifies the Estrogen Receptor 1 (ESR1) Gene and hsa-miR-26a-5p as Potential Prognostic Biomarkers in Patients with Intrahepatic Cholangiocarcinoma.", "doi": "10.12659/MSM.921815", "pmid": "32435051", "authors": ["Xianzheng Qin", "Yuning Song"], "journal": "Medical science monitor : international medical journal of experimental and clinical research", "year": 2020, "abstract": "BACKGROUND Intrahepatic cholangiocarcinoma arises from the epithelial cells of the bile ducts and is associated with poor prognosis. This study aimed to use bioinformatics analysis to identify molecular biomarkers of intrahepatic cholangiocarcinoma and their potential mechanisms. MATERIAL AND METHODS MicroRNA (miRNA) and mRNA microarrays from GSE53870 and GSE32879 were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed miRNAs (DEMs) associated with prognosis were identified using limma software and Kaplan-Meier survival analysis. Predictive target genes of the DEMs were identified using miRWalk, miRTarBase, miRDB, and TargetScan databases of miRNA-binding sites and targets. Target genes underwent Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Hub genes were analyzed by constructing the protein-protein interaction (PPI) network using Cytoscape. DEMs validated the hub genes, followed by construction of the miRNA-gene regulatory network. RESULTS Twenty-five DEMs were identified. Fifteen DEMs were upregulated, and ten were down-regulated. Kaplan-Meier survival analysis identified seven upregulated DEMs and nine down-regulated DEMs that were associated with the overall survival (OS), and 130 target genes were selected. GO analysis showed that target genes were mainly enriched for metabolism and development processes. KEGG analysis showed that target genes were mainly enriched for cancer processes and some signaling pathways. Fourteen hub genes identified from the PPI network were associated with the regulation of cell proliferation. The overlap between hub genes and DEMs identified the estrogen receptor 1 (ESR1) gene and hsa-miR-26a-5p. CONCLUSIONS Bioinformatics analysis identified ESR1 and hsa-miR-26a-5p as potential prognostic biomarkers for intrahepatic cholangiocarcinoma.", "claims": [{"id": "claim-method", "statement": "The limma package (version 3.40.6) (http://bioconductor.org/) was used to screen the DEMs and differentially expressed mRNAs. 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P-value) and the Benjamini–Hochberg false discovery rate (FDR) were used in the analysis to reduce the rate of false positives."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:32435051"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "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": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32435051", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.12659/MSM.921815", "sha256": "sha256:991c43e19f845f4658f2e17f6b4882980635c0eaa7c2dbd3db38c2ed7e3846c2", "bytes": 28831, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.12659/MSM.921815", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7257878", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}], "gaps": []}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The limma package (version 3.40.6) (http://bioconductor.org/) was used to screen the DEMs and differentially expressed mRNAs. 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