Analysis of long noncoding gene expression and its interactions with protein-coding genes in vascular endothelial cells in keloids.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39920823", "kind": "science-record", "revision": 4, "content_hash": "sha256:c6664ab0221a326e57037064718b38bff9d1b3d3ae54efe7c7f1bcd75d1b511c", "created_at": "2026-11-01T20:30:11Z", "updated_at": "2026-11-01T22:56:06Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Analysis of long noncoding gene expression and its interactions with protein-coding genes in vascular endothelial cells in keloids.", "doi": "10.1186/s40001-025-02271-6", "pmid": "39920823", "authors": ["Yunxiang Luo", "Zi Ye", "Yi Li", "Chau Wei Wong", "Shuqia Xu", "Yu Deng", "Zhicheng Su", "Xueqing Li", "Yingxiong Huang", "Bing Han"], "journal": "European journal of medical research", "year": 2025, "abstract": "OBJECTIVES: The purpose of this study was to determine the relationship between protein-coding RNA (messenger RNA, mRNA) and long noncoding RNA (lncRNA) expressed in vascular endothelial cells (VECs) in keloids by reanalyzing Gene Expression Omnibus (GEO) microarray chip data.\nMATERIALS AND METHODS: The GSE121618 database and clinical information of these samples were downloaded and reanalyzed by the R language package. Expression differences in mRNA and lncRNA between keloids and normal skin were calculated. GO/KEGG enrichment analysis was conducted to determine the function of these genes, and an interaction network of lncRNAs-mRNAs was constructed. Magnetic Sorting of VECs and qRT-PCR were used to verify these bioinformatic results.\nRESULTS: The expression of three hundred and five mRNAs in the keloid group was significantly different from that in the normal group, and 98 lncRNAs were different, 21 of which were upregulated and 118 of which were downregulated. The hub relationship between the upregulated lncRNA‒mRNA interaction was lncRNA LINC01546-RASAL3/COL13A1, while the downregulated hub was lncRNA LOC101929787-PRKAA2/KRT71/SSTR1. qPCR verification result showed no obvious statistical differences.\nCONCLUSIONS: Through the in-depth mining of keloid microarray data using bioinformatic methods, we speculated that VECs can affect the development and progression of keloids by epigenomic regulation via lncRNA‒mRNA interactions.", "claims": [{"id": "claim-method", "statement": "R package limma were chosen to perform gene differential expression analysis. The cut off of significant differential expressed mRNA and lncRNA were set as abs (fold changes) > 1.5 and P.adjust < 0.05 and filtered out differentially expressed mRNAs (DEmRNAs) and lncRNAs (DElncRNAs) were obtained. DEmRNAs were chosen as the candidate genelist, and the significance level of each GO/KEGG term was calculated using the Fisher test. First, the Pearson correlation coefficient (PCC) among DElncRNA and DEmRNA were calculated, and PCC > 0.95 were used as the cutoff threshold of significant DEmRNA–DElncRNA correlated pairs.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39920823", "locator": "sections[4] \"Download and preprocess of raw data\" paragraph 2", "quote": "R package limma were chosen to perform gene differential expression analysis."}, {"asset": "source:pmid:39920823", "locator": "sections[4] \"Download and preprocess of raw data\" paragraph 2", "quote": "The cut off of significant differential expressed mRNA and lncRNA were set as abs (fold changes) > 1.5 and P.adjust < 0.05 and filtered out differentially expressed mRNAs (DEmRNAs) and lncRNAs (DElncRNAs) were obtained."}, {"asset": "source:pmid:39920823", "locator": "sections[5] \"Functional enrichment analysis of DEmRNA\" paragraph 2", "quote": "DEmRNAs were chosen as the candidate genelist, and the significance level of each GO/KEGG term was calculated using the Fisher test."}, {"asset": "source:pmid:39920823", "locator": "sections[6] \"LncRNA‒mRNA correlation analysis and network mapping\" paragraph 2", "quote": "First, the Pearson correlation coefficient (PCC) among DElncRNA and DEmRNA were calculated, and PCC > 0.95 were used as the cutoff threshold of significant DEmRNA–DElncRNA correlated pairs."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data underlying this article was obtained from the NCBI GEO database (http://www.ncbi.nlm.nih.gov/geo) as follows: GSE121618 data. The platform of the chip data was Agilent-072363 SurePrint G3 Human GE v3 8 × 60 K Microarray.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39920823", "locator": "sections[25] \"Availability of data and materials\" paragraph 2", "quote": "The data underlying this article was obtained from the NCBI GEO database (http://www.ncbi.nlm.nih.gov/geo) as follows: GSE121618 data. The platform of the chip data was Agilent-072363 SurePrint G3 Human GE v3 8 × 60 K Microarray."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The expression of 305 mRNAs and 98 lncRNAs was significantly different in keloid VECs compared with normal-skin VECs.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39920823", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "The expression of three hundred and five mRNAs in the keloid group was significantly different from that in the normal group, and 98 lncRNAs were different, 21 of which were upregulated and 118 of which were downregulated."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The expression of 305 mRNAs and 98 lncRNAs was significantly different in keloid VECs compared with normal-skin VECs.", "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:39920823"], "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:GSE121618"], "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:GSE121618"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39920823", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s40001-025-02271-6", "sha256": "sha256:e52bdd35179d7895bc9dce1a546af0ab3baa2d055adc7e9b33b821744ea1220c", "bytes": 32088, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s40001-025-02271-6", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11806810", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE121618", "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=GSE121618", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE121618", "version": null, "note": "The data underlying this article was obtained from the NCBI GEO database (http://www.ncbi.nlm.nih.gov/geo) as follows: GSE121618 data. The platform of the chip data was Agilent-072363 SurePrint G3 Human GE v3 8 × 60 K Microarray.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data underlying this article was obtained from the NCBI GEO database (http://www.ncbi.nlm.nih.gov/geo) as follows: GSE121618 data. The platform of the chip data was Agilent-072363 SurePrint G3 Human GE v3 8 × 60 K Microarray.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3440194", "GSM3440195", "GSM3440196", "GSM3440197", "GSM3440198", "GSM3440199", "GSM3440200", "GSM3440201", "GSM3440202", "GSM3440203", "GSM3440204"], "sample_count": 11, "group_sizes": null, "group_sizes_basis": null, "platform": "21185", "taxon": "Homo sapiens", "title": "Expression Profile of Isolated Endothelial cells in Human Keloids: A microarray analysis", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE121618 not downloaded", "asset:data:geo:GSE121618 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "reordered", "quote": "R package limma were chosen to perform gene differential expression analysis. 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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": ["GSE121618"], "resolved_accessions": ["GSE121618"], "statements": ["The data underlying this article was obtained from the NCBI GEO database (http://www.ncbi.nlm.nih.gov/geo) as follows: GSE121618 data. The platform of the chip data was Agilent-072363 SurePrint G3 Human GE v3 8 × 60 K Microarray."], "basis": "The paper names GSE121618 in NCBI Gene Expression Omnibus (GEO) and the accession resolves in the repository. 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MATERIALS AND METHODS: The GSE121", "SIONS: Through the in-depth mining of keloid microarray data using bioinformatic methods, we specula", "ent-072363 SurePrint G3 Human GE v3 8 × 60 K Microarray."], "order_basis": "paper_text_order:343", "id": "assay:1"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["was lncRNA LOC101929787-PRKAA2/KRT71/SSTR1. qPCR verification result showed no obvious statis"], "order_basis": "paper_text_order:1244", "id": "assay:2"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["R package limma were chosen to perform gene differential expression analysis. The cut off of significant differential expressed mRNA and lncRNA were set as abs (fold changes) > 1.5 and P.adjust < 0.05 and filtered out differentially expressed mRNAs (DEmRNAs) and lncRNAs (DElncRNAs) were obtained. DEmRNAs were chosen as the candidate genelist, and the significance level of each GO/KEGG term was calculated using the Fisher test. First, the Pearson correlation coefficient (PCC) among DElncRNA and DEmRNA were calculated, and PCC > 0.95 were used as the cutoff threshold of significant DEmRNA–DElncRNA correlated pairs."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}