Identification of the differentially expressed activated memory CD4+ T-cells-related genes and ceRNAs in oral lichen planus.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39022110", "kind": "science-record", "revision": 4, "content_hash": "sha256:11151f699d25d54e562941f29859e6ac0ef7e891893a48decb34f14cbccf1b5f", "created_at": "2026-11-01T20:29:06Z", "updated_at": "2026-11-01T22:54:43Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of the differentially expressed activated memory CD4+ T-cells-related genes and ceRNAs in oral lichen planus.", "doi": "10.1016/j.heliyon.2024.e33305", "pmid": "39022110", "authors": ["Hui Zhu", "Huanping Lu", "Tianyou Li", "Jing Chen"], "journal": "Heliyon", "year": 2024, "abstract": "Background: Oral lichen planus (OLP) is a common chronic oral mucosal disease with 1.4 % malignant transformation rate, and its etiology especially immune pathogenesis remains unclear. This study was aimed at investigating the immune cells related molecular underlying the pathophysiology of OLP through bioinformatics analysis.\nMethods: The dataset GSE52130 obtained from the Gene Expression Omnibus (GEO) database was conducted a comprehensive analysis in this study. The CIBERSORTx was used for investigating immune cells infiltration. The gene set enrichment analysis (GSEA) and gene ontology (GO) enrichment were performed for exploring the biological functions and gene annotation. The protein-protein interactions (PPI) were constructed by STRING database and visualized by Cytoscape software. The cytohubba plugin was utilized for screening hub genes. The receiver operating characteristic (ROC) was performed for evaluating diagnostic value of hub genes. The miRNAs, lncRNAs and drugs were respectively predicted by NetworkAnalyst, miRTarbase, ENCORI, and DGIdb database.\nResults: This study identified 595 differentially expressed genes (DEGs). The GSEA indicated keratinization, innate immune system and biological oxidation were involved in OLP. GO analysis showed extracellular matrix and keratinocyte were mainly enriched. And we found the activated memory CD4+ T cells were lowly infiltrated in OLP. We identified 101 activated memory CD4+ T-cells-related DEGs. Three hub genes (APP, IL1B, TF) were selected. APP and IL1B were significantly up-regulated, whereas TF was down-regulated in OLP. The three hub genes show high diagnostic value in OLP. Additionally, they were involved in MAPK signal, NF-kappaB signal and iron metabolism in OLP. What's more, NEAT1/XIST - miR - 15a - 5p/miR - 155-5p - APP/IL1B signal axis was focused in competing endogenous RNA (ceRNA) network. In addition, 35 drugs were predicted for OLP.\nConclusion: Three activated memory CD4+ T-cells-related DEGs were identified by integrative analysis. It may provide novel insight into the pathogenesis of OLP and suggest potential therapeutic targets for OLP.", "claims": [{"id": "claim-method", "statement": "According to sample information of the dataset GSE52130, the samples were divided into normal and OLPE groups, then we analyzed the difference between the two groups by R (v4.2.1) package limma [12], and used Benjamini-Hochberg method to adjust p-values for multiple testing.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39022110", "locator": "sections[4] \"Identification of differentially expressed genes (DEGs)\" paragraph 2", "quote": "According to sample information of the dataset GSE52130, the samples were divided into normal and OLPE groups, then we analyzed the difference between the two groups by R (v4.2.1) package limma [12], and used Benjamini-Hochberg method to adjust p-values for multiple testing."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated and analyzed in this study are available GEO (https://www.ncbi.nlm.nih.gov/geo/) databases. All data mentioned in the manuscript can be provided by the corresponding author upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39022110", "locator": "sections[23] \"Data availability statement\" paragraph 2", "quote": "The datasets generated and analyzed in this study are available GEO (https://www.ncbi.nlm.nih.gov/geo/) databases. All data mentioned in the manuscript can be provided by the corresponding author upon reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The APP, IL1B and TF hub genes showed high diagnostic value for OLP, with AUCs of 1.000, 1.000 and 0.898, respectively.", "kind": "quantitative", "target": {"value": 1.0, "unit": "auc", "tolerance": null, "source": "The results suggested the APP, IL1B and TF showed the high diagnostic value with the AUC of 1.000, 1.000 and 0.898, respectively."}, "evidence": [{"asset": "source:pmid:39022110", "locator": "sections[18] \"Diagnostic value of the hub genes\" paragraph 2", "quote": "The results suggested the APP, IL1B and TF showed the high diagnostic value with the AUC of 1.000, 1.000 and 0.898, respectively."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The APP, IL1B and TF hub genes showed high diagnostic value for OLP, with AUCs of 1.000, 1.000 and 0.898, respectively.", "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:39022110"], "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:GSE52130"], "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:GSE52130"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39022110", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.heliyon.2024.e33305", "sha256": "sha256:d52a327ca230e26ee6e716f3e341b7c300719507b7f9ea4719ccf4fdce00d27e", "bytes": 27950, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.heliyon.2024.e33305", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11252958", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE52130", "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=GSE52130", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE52130", "version": null, "note": "The datasets generated and analyzed in this study are available GEO (https://www.ncbi.nlm.nih.gov/geo/) databases. All data mentioned in the manuscript can be provided by the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated and analyzed in this study are available GEO (https://www.ncbi.nlm.nih.gov/geo/) databases. 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No tolerance is published because the paper states none."}], "gaps": ["method.reader_differs_from_extractor"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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