Construction and analysis of a lncRNA-miRNA-mRNA network based on competitive endogenous RNA reveal functional lncRNAs in oral cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32571304", "kind": "science-record", "revision": 7, "content_hash": "sha256:eb5bf16ca9b573f8ebe39156c805cc2d151b3a503eaeee69b8a7c3dac5e492ff", "created_at": "2026-11-01T15:41:04Z", "updated_at": "2026-11-01T22:01:46Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Construction and analysis of a lncRNA-miRNA-mRNA network based on competitive endogenous RNA reveal functional lncRNAs in oral cancer.", "doi": "10.1186/s12920-020-00741-w", "pmid": "32571304", "authors": ["Junhao Yin", "Xiaoli Zeng", "Zexin Ai", "Miao Yu", "Yang'ou Wu", "Shengjiao Li"], "journal": "BMC medical genomics", "year": 2020, "abstract": "BACKGROUND: A growing evidence suggests that long non-coding RNAs (lncRNAs) can function as a microRNA (miRNA) sponge in various diseases including oral cancer. However, the pathophysiological function of lncRNAs remains unclear.\nMETHODS: Based on the competitive endogenous RNA (ceRNA) theory, we constructed a lncRNA-miRNA-mRNA network in oral cancer with the human expression profiles GSE74530 from the Gene Expression Omnibus (GEO) database. We used topological analysis to determine the hub lncRNAs in the regulatory ceRNA network. Then, function enrichment analysis was performed using the clusterProfiler R package. Clinical information was downloaded from The Cancer Genome Atlas (TCGA) database and survival analysis was performed with Kaplan-Meier analysis.\nRESULTS: A total of 238 potential co-dysregulated competing triples were obtained in the lncRNA-associated ceRNA network in oral cancer, which consisted of 10 lncRNA nodes, 41 miRNA nodes and 122 mRNA nodes. Additionally, we found lncRNA HCG22 exhibiting superior potential as a diagnostic and prognostic marker of oral cancer.\nCONCLUSIONS: Our findings provide novel insights to understand the ceRNA regulation in oral cancer and identify a novel lncRNA as a potential molecular biomarker.", "claims": [{"id": "claim-method", "statement": "Survival analysis was estimated based on Kaplan-Meier curve analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32571304", "locator": "sections[21] \"Survival analysis\" paragraph 2", "quote": "Survival analysis was estimated based on Kaplan-Meier curve analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets supporting the conclusions of this article were retrieved from the GEO repository (https://www.ncbi.nlm.nih.gov/geo/) with the accession number GSE74530 and the series matrix files were available at (ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74530/matrix/). The raw data for data quality assessment was available at (https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE74530&format=file). The full data table of microarray platform GPL570 was available at (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL570). The human comprehensive gene annotation we used to identify lncRNAs was available at (ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz). The case IDs and direct web links of all oral cancer samples obtained from the TCGA data portal (http://portal.gdc.cancer.gov/; dbGaP Study Accession: phs000178) by Bioconductor package TCGAbiolinks were shown in Additional file 2. Data banks/repositories corresponding to all datasets analyzed in this study were listed in Additional file 1.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32571304", "locator": "sections[30] \"Availability of data and materials\" paragraph 2", "quote": "The datasets supporting the conclusions of this article were retrieved from the GEO repository (https://www.ncbi.nlm.nih.gov/geo/) with the accession number GSE74530 and the series matrix files were available at (ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74530/matrix/). The raw data for data quality assessment was available at (https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE74530&format=file). The full data table of microarray platform GPL570 was available at (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL570). The human comprehensive gene annotation we used to identify lncRNAs was available at (ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz). The case IDs and direct web links of all oral cancer samples obtained from the TCGA data portal (http://portal.gdc.cancer.gov/; dbGaP Study Accession: phs000178) by Bioconductor package TCGAbiolinks were shown in Additional file 2. Data banks/repositories corresponding to all datasets analyzed in this study were listed in Additional file 1."}], "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:32571304"], "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:GSE74530"], "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:GSE74530"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32571304", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12920-020-00741-w", "sha256": "sha256:c1aa0e0df2a16357c0997658996807ac2d3d0d83fd491317c9494c07326dcdf8", "bytes": 50014, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12920-020-00741-w", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7310129", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE74530", "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=GSE74530", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE74530", "version": null, "note": "The datasets supporting the conclusions of this article were retrieved from the GEO repository (https://www.ncbi.nlm.nih.gov/geo/) with the accession number GSE74530 and the series matrix files were available at (ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74530/matrix/). The raw data for data quality assessment was available at (https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE74530&format=file). The full data table of microarray platform GPL570 was available at (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL570). The human comprehensive gene annotation we used to identify lncRNAs was available at (ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz). The case IDs and direct web links of all oral cancer samples obtained from the TCGA data portal (http://portal.gdc.cancer.gov/; dbGaP Study Accession: phs000178) by Bioconductor package TCGAbiolinks were shown in Additional file 2. 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE74530"], "resolved_accessions": ["GSE74530"], "statements": ["The datasets supporting the conclusions of this article were retrieved from the GEO repository (https://www.ncbi.nlm.nih.gov/geo/) with the accession number GSE74530 and the series matrix files were available at (ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74530/matrix/). The raw data for data quality assessment was available at (https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE74530&format=file). The full data table of microarray platform GPL570 was available at (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL570). The human comprehensive gene annotation we used to identify lncRNAs was available at (ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz). The case IDs and direct web links of all oral cancer samples obtained from the TCGA data portal (http://portal.gdc.cancer.gov/; dbGaP Study Accession: phs000178) by Bioconductor package TCGAbiolinks were shown in Additional file 2. Data banks/repositories corresponding to all datasets analyzed in this study were listed in Additional file 1."], "basis": "The paper names GSE74530 in NCBI Gene Expression Omnibus (GEO) and the accession resolves in the repository. 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