Construction for Long Non-Coding RNA (lncRNA)-Associated Competing Endogenous RNA (ceRNA) Network in Human Retinal Detachment (RD) with Proliferative Vitreoretinopathy (PVR).

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32103829", "kind": "science-record", "revision": 9, "content_hash": "sha256:77eb58c1a2bbe9d5f7b6a10143537b8a63a3f1210e0b5f850fdea9dd179bb18b", "created_at": "2026-11-01T15:40:57Z", "updated_at": "2026-11-01T22:44:36Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Construction for Long Non-Coding RNA (lncRNA)-Associated Competing Endogenous RNA (ceRNA) Network in Human Retinal Detachment (RD) with Proliferative Vitreoretinopathy (PVR).", "doi": "10.12659/MSM.919871", "pmid": "32103829", "authors": ["Ke Yao", "Yixian Yu", "Hong Zhang"], "journal": "Medical science monitor : international medical journal of experimental and clinical research", "year": 2020, "abstract": "BACKGROUND The aim of this study was to analyze the long non-coding RNA (lncRNA)-associated competing endogenous RNA (ceRNA) network in human retinal tissues following detachment with proliferative vitreoretinopathy (PVR). MATERIAL AND METHODS Expression data of 19 human detached retinas with PVR and 19 normal retinas from postmortem donors were downloaded from Gene Expression Omnibust (GEO) database (GSE28133). The R package \"limma\" was utilized to discriminate the dysregulated lncRNA and mRNA profiles. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of differentially expressed mRNAs were performed using R packages \"Clusterprofiler.\" The ceRNA network of dysregulated genes was constructed by using mircode, miRDB, miRTarBase and TargetScan databases, and was visualized by Cytoscape v3.6.1. RESULTS A total of 23 lncRNAs and 994 mRNAs were identified significantly expressed between the human detached retinas with PVR and the normal retina tissues, with thresholds of |log₂FoldChange| >1.0 and adjusted P-value <0.05. The constructed ceRNA network (lncRNA-miRNA-mRNA regulatory axis) included 9 PVR-specific lncRNAs, as well as 27 miRNAs and 73 mRNAs. CONCLUSIONS We demonstrated the differential lncRNA expression profile and constructed a lncRNA-associated ceRNA network in human detached retinas with PVR. This may ferret out an unknown ceRNA regulatory network in human retinal detachment with PVR.", "claims": [{"id": "claim-method", "statement": "We used the “limma” package in R software to identify the differentially expressed genes (lncRNAs and mRNAs) between human detached retinas with PVR and the control group, with |log2FoldChange (FC)|>1.0 and adjusted P-value <0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32103829", "locator": "sections[4] \"Differentially expressed gene analysis\" paragraph 2", "quote": "We used the “limma” package in R software to identify the differentially expressed genes (lncRNAs and mRNAs) between human detached retinas with PVR and the control group, with |log2FoldChange (FC)|>1.0 and adjusted P-value <0.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The RNA expression data of tissue samples were obtained from GEO database. The dataset (GSE28133) contained 19 specimens from patients for severe retinal detachment with PVR and 19 normal control retina specimens from postmortem donors. Clinical and pathological features of patients were described [2]. All the samples were analyzed using Affymetrix Human Genome U133 Plus 2.0 Array.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32103829", "locator": "sections[3] \"Tissue samples from the GEO database and bioinformatics analysis\" paragraph 2", "quote": "The RNA expression data of tissue samples were obtained from GEO database. The dataset (GSE28133) contained 19 specimens from patients for severe retinal detachment with PVR and 19 normal control retina specimens from postmortem donors. Clinical and pathological features of patients were described [2]. All the samples were analyzed using Affymetrix Human Genome U133 Plus 2.0 Array."}], "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:32103829"], "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:GSE28133"], "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:GSE28133"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32103829", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.12659/MSM.919871", "sha256": "sha256:7c18ca47c509f98496b9907d75af088d8ae835d593b7a7b3094b93a99c8db1ff", "bytes": 22537, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.12659/MSM.919871", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7061588", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE28133", "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=GSE28133", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE28133", "version": null, "note": "The RNA expression data of tissue samples were obtained from GEO database. The dataset (GSE28133) contained 19 specimens from patients for severe retinal detachment with PVR and 19 normal control retina specimens from postmortem donors. Clinical and pathological features of patients were described [2]. All the samples were analyzed using Affymetrix Human Genome U133 Plus 2.0 Array.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The RNA expression data of tissue samples were obtained from GEO database. The dataset (GSE28133) contained 19 specimens from patients for severe retinal detachment with PVR and 19 normal control retina specimens from postmortem donors. Clinical and pathological features of patients were described [2]. All the samples were analyzed using Affymetrix Human Genome U133 Plus 2.0 Array.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM697014", "GSM697015", "GSM697016", "GSM697017", "GSM697018", "GSM697019", "GSM697020", "GSM697021", "GSM697022", "GSM697023", "GSM697024", "GSM697025", "GSM697026", "GSM697027", "GSM697028", "GSM697029", "GSM697030", "GSM697031", "GSM697032", "GSM697033", "GSM697034", "GSM697035", "GSM697036", "GSM697037", "GSM697038", "GSM697039", "GSM697040", "GSM697041", "GSM697042", "GSM697043", "GSM697044", "GSM697045", "GSM697046", "GSM697047", "GSM697048", "GSM697049", "GSM697050", "GSM697051"], "sample_count": 38, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Transcriptomic analysis of human retinal detachment (RD) reveals both inflammation and photoreceptor death", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": 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