Comprehensive Identification of Potential Crucial Genes and miRNA-mRNA Regulatory Networks in Papillary Thyroid Cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33521130", "kind": "science-record", "revision": 7, "content_hash": "sha256:d10e2813d020d619368bf811b7ce32ef877eb2884dd1dd7e7241cc748584bf24", "created_at": "2026-11-01T15:41:24Z", "updated_at": "2026-11-01T22:03:01Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comprehensive Identification of Potential Crucial Genes and miRNA-mRNA Regulatory Networks in Papillary Thyroid Cancer.", "doi": "10.1155/2021/6752141", "pmid": "33521130", "authors": ["Ben-Yu Nan", "Guo-Feng Xiong", "Zi-Rui Zhao", "Xi Gu", "Xin-Sheng Huang"], "journal": "BioMed research international", "year": 2021, "abstract": "BACKGROUND: Thyroid cancer is the most common endocrine malignancy, with a recent global increase of 20% in age-related incidence. Ultrasonography and ultrasonography-guided fine-needle aspiration biopsy (FNAB) are the most widely used diagnostic tests for thyroid nodules; however, it is estimated that up to 25% of thyroid biopsies are cytologically inconclusive. Molecular markers can help guide patient-oriented and targeted treatment of thyroid nodules and thyroid cancer.\nMETHODS: Datasets related to papillary thyroid cancer (PTC) or thyroid carcinoma (GSE129562, GSE3678, GSE54958, GSE138042, and GSE124653) were downloaded from the GEO database and analysed using the Limma package of R software. For functional enrichment analysis, the Kyoto Encyclopedia of Genes and Genomes pathway analysis and Gene Ontology were applied to differentially expressed genes (DEGs) using the Metascape website. A protein-protein interaction (PPI) network was built from the STRING database. Gene expression, protein expression, immunohistochemistry, and potential functional gene survival were analysed using the GEPIA website, the Human Protein Atlas website, and the UALCAN website. Potential target miRNAs were predicted using the miRDB and Starbase datasets.\nRESULTS: We found 219 upregulated and 310 downregulated DEGs, with a cut-off of p < 0.01 and ∣log FC | >1.5. The DEGs in papillary thyroid cancer were mainly enriched in extracellular structural organisation. At the intersection of the PPI network and Metascape MCODEs, the hub genes in common were identified as FN1, APOE, CLU, and SDC2. In the targeted regulation network of miRNA-mRNA, the hsa-miR-424-5p was found to synchronously modulate two hub genes. Survival analysis showed that patients with high expression of CLU and APOE had better prognosis.\nCONCLUSIONS: CLU and APOE are involved in the molecular mechanism of papillary thyroid cancer. The hsa-miR-424-5p might have the potential to reverse the processes of papillary thyroid cancer by modulating the hub genes. These are potential targets for the treatment of patients with papillary thyroid cancer.", "claims": [{"id": "claim-method", "statement": "A survival analysis of the hub genes was performed using the Human Protein Atlas online tool, and expression was analysed using the GEPIA website, which helped us to investigate the correlation between hub genes and survival of patients with thyroid cancer.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33521130", "locator": "sections[14] \"3.4. Analysis of Hub Genes by Survival Analysis and Expression\" paragraph 2", "quote": "A survival analysis of the hub genes was performed using the Human Protein Atlas online tool, and expression was analysed using the GEPIA website, which helped us to investigate the correlation between hub genes and survival of patients with thyroid cancer."}], "state": "complete"}, {"id": "claim-data-access", "statement": "GSE129562, GSE3678, GSE54958, GSE138042, and GSE124653 were downloaded from the Gene Expression Omnibus.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33521130", "locator": "sections[20] \"Data Availability\" paragraph 2", "quote": "GSE129562, GSE3678, GSE54958, GSE138042, and GSE124653 were downloaded from the Gene Expression Omnibus."}], "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:33521130"], "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:GSE124653"], "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:GSE124653"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33521130", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2021/6752141", "sha256": 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