Construction of a Potential Breast Cancer-Related miRNA-mRNA Regulatory Network.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33204705", "kind": "science-record", "revision": 8, "content_hash": "sha256:c01e3a85cc13ca31cc03f44aa6ed5b77b273aa2c8e619ab298ecb4dc9f6f222b", "created_at": "2026-11-01T15:41:16Z", "updated_at": "2026-11-01T22:45:38Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Construction of a Potential Breast Cancer-Related miRNA-mRNA Regulatory Network.", "doi": "10.1155/2020/6149174", "pmid": "33204705", "authors": ["Xinhong Liu", "Feng Chen", "Fang Tan", "Fang Li", "Ruokun Yi", "Dingyi Yang", "Xin Zhao"], "journal": "BioMed research international", "year": 2020, "abstract": "BACKGROUND: Breast cancer is a malignant tumor that occurs in the epithelial tissue of the breast gland and has become the most common malignancy in women. The regulation of the expression of related genes by microRNA (miRNA) plays an important role in breast cancer. We constructed a comprehensive breast cancer-miRNA-gene interaction map.\nMETHODS: Three miRNA microarray datasets (GSE26659, GSE45666, and GSE58210) were obtained from the GEO database. Then, the R software \"LIMMA\" package was used to identify differential expression analysis. Potential transcription factors and target genes of screened differentially expressed miRNAs (DE-miRNAs) were predicted. The BRCA GE-mRNA datasets (GSE109169 and GSE139038) were downloaded from the GEO database for identifying differentially expressed genes (DE-genes). Next, GO annotation and KEGG pathway enrichment analysis were conducted. A PPI network was then established, and hub genes were identified via Cytoscape software. The expression and prognostic roles of hub genes were further evaluated.\nRESULTS: We found 6 upregulated differentially expressed- (DE-) miRNAs and 18 downregulated DE-miRNAs by analyzing 3 Gene Expression Omnibus databases, and we predicted the upstream transcription factors and downstream target genes for these DE-miRNAs. Then, we used the GEO database to perform differential analysis on breast cancer mRNA and obtained differentially expressed mRNA. We found 10 hub genes of upregulated DE-miRNAs and 10 hub genes of downregulated DE-miRNAs through interaction analysis.\nCONCLUSIONS: In this study, we have performed an integrated bioinformatics analysis to construct a more comprehensive BRCA-miRNA-gene network and provide new targets and research directions for the treatment and prognosis of BRCA.", "claims": [{"id": "claim-method", "statement": "The R software “LIMMA” package was used to identify DE-miRNAs between BRCA tissues and normal tissues.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33204705", "locator": "sections[4] \"2.2. Identification of Differentially Expressed miRNAs (DE-miRNAs)\" paragraph 2", "quote": "The R software “LIMMA” package was used to identify DE-miRNAs between BRCA tissues and normal tissues."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data used to support the study findings are mostly included in the article. It is available from the corresponding authors upon request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33204705", "locator": "sections[31] \"Data Availability\" paragraph 2", "quote": "The data used to support the study findings are mostly included in the article. It is available from the corresponding authors upon request."}], "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:33204705"], "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:GSE109169"], "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:GSE109169"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33204705", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2020/6149174", "sha256": "sha256:7e071a2bfc27f1f62413ed526bd4390469ad93607a78671011e58d62a431a7ea", "bytes": 51506, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2020/6149174", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7657683", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE109169", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE109169", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE109169", "version": null, "note": "The data used to support the study findings are mostly included in the article. 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