Identification of Genes Related to Endoplasmic Reticulum Stress (ERS) in Chronic Obstructive Pulmonary Disease (COPD) and Clinical Validation.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38162988", "kind": "science-record", "revision": 4, "content_hash": "sha256:042b9f9e54dd0ae8172a565319e060c3ba4d62bb93451b4ee2178853d3a0a3d3", "created_at": "2026-11-01T19:20:05Z", "updated_at": "2026-11-01T22:53:22Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Genes Related to Endoplasmic Reticulum Stress (ERS) in Chronic Obstructive Pulmonary Disease (COPD) and Clinical Validation.", "doi": "10.2147/COPD.S440692", "pmid": "38162988", "authors": ["Siming Tao", "Jing Jing", "Yide Wang", "Fengsen Li", "Hongxia Ma"], "journal": "International journal of chronic obstructive pulmonary disease", "year": 2023, "abstract": "Objective: Endoplasmic reticulum stress (ERS) is key in chronic obstructive pulmonary disease (COPD) incidence and progression. This study aims to identify potential ERS-related genes in COPD through bioinformatics analysis and clinical experiments.\nMethods: We first obtained a COPD-related mRNA expression dataset (GSE38974) from the Gene Expression Omnibus (GEO) database. The R software was then used to identify potential differentially expressed genes (DEGs) of COPD-related ERS (COPDERS). Subsequently, the identified DEGs were subjected to protein-protein interaction (PPI), correlation, Gene Ontology (GO) enrichment, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. Following that, qRT-PCR was used to examine the RNA expression of six ERS-related DEGs in blood samples obtained from the COPD and control groups. The genes were also subjected to microRNA analysis. Finally, a correlation analysis was performed between the DEGs and key clinical indicators.\nResults: Six ERS-related DEGs (five upregulated and one downregulated) were identified based on samples drawn from 23 COPD patients and nine healthy individuals enrolled in the study. Enrichment analysis revealed multiple ERS-related pathways. The qRT-PCR and mRNA microarray bioinformatics analysis results showed consistent STC2, APAF1, BAX, and PTPN1 expressions in the COPD and control groups. Additionally, hsa-miR-485-5p was identified through microRNA prediction and DEG analysis. A correlation analysis between key genes and clinical indicators in COPD patients demonstrated that STC2 was positively and negatively correlated with eosinophil count (EOS) and lymphocyte count (LYM), respectively. On the other hand, PTPN1 showed a strong correlation with pulmonary function indicators.\nConclusion: Four COPDERS-related key genes (STC2, APAF1, BAX, and PTPN1) were identified through bioinformatics analysis and clinical validation, and the expressions of some genes exhibited a significant correlation with the selected clinical indicators. Furthermore, hsa-miR-485-5p was identified as a potential key target in COPDERS, but its precise mechanism remains unclear.", "claims": [{"id": "claim-method", "statement": "The “limma” package in R software was used to identify ERS-related differentially expressed genes (DEGs).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38162988", "locator": "sections[3] \"Analysis of ERS-Related DEGs\" paragraph 2", "quote": "The “limma” package in R software was used to identify ERS-related differentially expressed genes (DEGs)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The corresponding authors will provide Supplemental Material and all other data used this study upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38162988", "locator": "sections[18] \"Data Sharing Statement\" paragraph 2", "quote": "The corresponding authors will provide Supplemental Material and all other data used this study upon reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Six ERS-related DEGs (five upregulated and one downregulated) were identified based on samples drawn from 23 COPD patients and nine healthy individuals enrolled in the study.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38162988", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Six ERS-related DEGs (five upregulated and one downregulated) were identified based on samples drawn from 23 COPD patients and nine healthy individuals enrolled in the study."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Six ERS-related DEGs (five upregulated and one downregulated) were identified based on samples drawn from 23 COPD patients and nine healthy individuals enrolled in the study.", "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:38162988"], "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:GSE38974"], "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:GSE38974"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38162988", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/COPD.S440692", "sha256": "sha256:864ed3eecc20a72e99dd2dc9135436c312d2fde19bc0c0ff8ae23f78ecc1b04d", "bytes": 27763, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/COPD.S440692", "version": null, "note": "Full article fetched from PMC; 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Human gammaherpesvirus 8; Human alphaherpesvirus 1; human gammaherpesvirus 4; Betapolyomavirus macacae; Homo sapiens; Human betaherpesvirus 5; Murid betaherpesvirus 1; Human immunodeficiency virus 1; Rattus norvegicus; JC polyomavirus; Murid gammaherpesvirus 4; Betapolyomavirus hominis", "title": "Gene expression networks in COPD: microRNA and mRNA regulation", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE38974 not downloaded", "asset:data:geo:GSE38974 licence not read"]}, "analysis": {"state": "partial", "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": "verbatim", "quote": "The “limma” package in R software was used to identify ERS-related differentially expressed genes (DEGs)."}}, {"id": "method-2", "family": "principal_component_analysis", "specific": "pca", "label": "Principal component analysis", "dsl_operations": ["pca_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["wide_numeric_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "Principal Component Analysis"}}, {"id": "method-3", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}, {"id": "method-4", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "pathway enrichment"}}], "targets": [], "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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The qRT-PCR and mRNA microarray bioinformatics analysis results showed consi", "platform (Agilent-014850 Whole Human Genome Microarray 4x44K G4112F) and contains 23 COPD and nine", "ed DEGs The normalized expression matrix for microarray data was first downloaded from GSE38974. The", "SE38974. Consistent with the results of mRNA microarray in lung tissue samples, the APAF1, BAX, PPP1"], "order_basis": "paper_text_order:1361", "id": "assay:1"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["that ERS-related DEGs mainly participated in apoptosis pathways related to JAK-STAT, TP53, IL-10, a", "teraction. (G) Interleukin 10 Signaling. (H) Apoptosis. (I) Photodynamic Therapy-induced Nfkb Survi", "Network. 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