Lumican as a potential biomarker for diabetic nephropathy.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40195568", "kind": "science-record", "revision": 4, "content_hash": "sha256:4976f86e79ba2cdee7e6e86868621cca12af492838b4ddf55e53c46f54009b65", "created_at": "2026-11-01T20:30:22Z", "updated_at": "2026-11-01T22:56:20Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Lumican as a potential biomarker for diabetic nephropathy.", "doi": "10.1080/0886022X.2025.2480245", "pmid": "40195568", "authors": ["Yuejia Tao", "Yipeng Liu", "Zunsong Wang", "Lijun Tang", "Ying Zhang", "Shanshan Zheng", "Ruixue Wang", "Kai Wei", "Shunyao Liu"], "journal": "Renal failure", "year": 2025, "abstract": "OBJECTIVE: We employed bioinformatics to identify potential biomarkers for diabetic nephropathy (DN) and investigate the role of the key gene lumican in its molecular processes.\nMETHODS: We analyzed the GSE96804 and GSE30528 DN datasets from the Gene Expression Omnibus (GEO). GO and GSEA-KEGG enrichment analyses were used to identify key biological functions and related pathways. Cytoscape software was used to screen differentially expressed genes (DEGs) to obtain hub genes. The Nephroseq database was used to analyze the effect of hub genes on renal function, and the importance of lumican, a gene potentially related to DN progression, was further examined in clinical samples. GO and KEGG analyses were performed on lumican and its interacting proteins to elucidate their main biological functions and related pathways.\nRESULTS: We identified 1139 DEGs. GO enrichment analysis revealed that the DEGs were mainly involved in responses to hexose, cell-cell junctions. GSEA-KEGG enrichment analysis indicated that the DEGs were related to amino acid metabolism, adipokine signaling. Nephroseq database analysis revealed that hub genes were upregulated in the kidney tissues of patients with DN and that their expression was negatively correlated with estimated glomerular filtration rate (eGFR). Lumican was among the top hub genes, and its expression was increased in renal tissues of DN patients as confirmed by immunohistochemistry and immunofluorescence. GO and KEGG enrichment analyses revealed that lumican and its interacting proteins were associated with extracellular matrix organization.\nCONCLUSION: Lumican is a potential biomarker for predicting DN and is closely related to the extracellular matrix. These findings provide novel insights into the clinical diagnosis and treatment of DN.", "claims": [{"id": "claim-method", "statement": "Differential analysis was conducted using the R language limma package with |logFC| > 1 and p < 0.05 as the screening criteria.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40195568", "locator": "sections[5] \"Filtering and functional annotation of DEGs\" paragraph 2", "quote": "Differential analysis was conducted using the R language limma package with |logFC| > 1 and p < 0.05 as the screening criteria."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data for this study are available from the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40195568", "locator": "sections[25] \"Data statement\" paragraph 2", "quote": "Data for this study are available from the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We identified 1139 DEGs.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40195568", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "We identified 1139 DEGs."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "We identified 1139 DEGs.", "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:40195568"], "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:GSE30528"], "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:GSE30528"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40195568", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1080/0886022X.2025.2480245", "sha256": "sha256:52d0591a6734077e475acf0f7a38881b9070155ba642e62c3cd6dfb850c970d8", "bytes": 21985, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1080/0886022X.2025.2480245", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11983523", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE30528", "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=GSE30528", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE30528", "version": null, "note": "Data for this study are available from the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data for this study are available from the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM756992", "GSM756993", "GSM756994", "GSM756995", "GSM756996", "GSM756997", "GSM756998", "GSM756999", "GSM757000", "GSM757001", "GSM757002", "GSM757003", "GSM757004", "GSM757005", "GSM757006", "GSM757007", "GSM757008", "GSM757009", "GSM757010", "GSM757011", "GSM757012", "GSM757013"], "sample_count": 22, "group_sizes": null, "group_sizes_basis": null, "platform": "571", "taxon": "Homo sapiens", "title": "Transcriptome Analysis of Human Diabetic Kidney Disease (DKD Glomeruli vs. Control Glomeruli)", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE96804", "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=GSE96804", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE96804", "version": null, "note": "Data for this study are available from the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data for this study are available from the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2544275", "GSM2544276", "GSM2544277", "GSM2544278", "GSM2544279", "GSM2544280", "GSM2544281", "GSM2544282", "GSM2544283", "GSM2544284", "GSM2544285", "GSM2544286", "GSM2544287", "GSM2544288", "GSM2544289", "GSM2544290", "GSM2544291", "GSM2544292", "GSM2544293", "GSM2544294", "GSM2544295", "GSM2544296", "GSM2544297", "GSM2544298", "GSM2544299", "GSM2544300", "GSM2544301", "GSM2544302", "GSM2544303", "GSM2544304", "GSM2544305", "GSM2544306", "GSM2544307", "GSM2544308", "GSM2544309", "GSM2544310", "GSM2544311", "GSM2544312", "GSM2544313", "GSM2544314", "GSM2544315", "GSM2544316", "GSM2544317", "GSM2544318", "GSM2544319", "GSM2544320", "GSM2544321", "GSM2544322", "GSM2544323", "GSM2544324", "GSM2544325", "GSM2544326", "GSM2544327", "GSM2544328", "GSM2544329", "GSM2544330", "GSM2544331", "GSM2544332", "GSM2544333", "GSM2544334", "GSM2544335"], "sample_count": 61, "group_sizes": null, "group_sizes_basis": null, "platform": "17586", "taxon": "Homo sapiens", "title": "Exon Level Expression Profiling of Diabetic Nephropathy", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE30528 not downloaded", "asset:data:geo:GSE30528 licence not read", "asset:data:geo:GSE96804 not downloaded", "asset:data:geo:GSE96804 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": "Differential analysis was conducted using the R language limma package with |logFC| > 1 and p < 0.05 as the screening criteria."}}, {"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": 0.8, "band": "high", "quote": "PPI"}}, {"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": "GO 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. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE96804", "GSE30528"], "resolved_accessions": ["GSE96804", "GSE30528"], "statements": ["Data for this study are available from the corresponding author."], "basis": "The paper names GSE96804, GSE30528 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:40195568", "data:geo:GSE30528"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE30528"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:49:45Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 6799, "completion_tokens": 1611, "cached_tokens": 256}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:40195568", "type": "paper", "label": "pmid:40195568"}, {"id": "source:pmid:40195568", "type": "manuscript", "label": "PMID 40195568 full text"}, {"id": "data:geo:GSE30528", "type": "dataset", "label": "GEO GSE30528"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:40195568", "type": "paper", "label": "pmid:40195568"}, {"id": "source:pmid:40195568", "type": "manuscript", "label": "PMID 40195568 full text"}, {"id": "data:geo:GSE30528", "type": "dataset", "label": "GEO GSE30528"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-40195568", "type": "extraction", "used": ["source:pmid:40195568"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE30528", "type": "accession_resolution", "used": ["data:geo:GSE30528"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:40195568", "parent_hash": "sha256:512e43dbb872b09eb0dbef13a8b4819e23483e6118951e7a1c5caa1337ac9145", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE30528 licence not read", "asset:data:geo:GSE30528 not downloaded", "asset:data:geo:GSE96804 licence not read", "asset:data:geo:GSE96804 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["renal tissues of DN patients as confirmed by immunohistochemistry and immunofluorescence. GO and KEGG enrichme", "nts as confirmed by immunohistochemistry and immunofluorescence. GO and KEGG enrichment analyses revealed th"], "order_basis": "paper_text_order:1433", "id": "assay:1"}, {"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["O database and screening the gene expression microarray datasets, we finally selected the gene expre"], "order_basis": "paper_text_order:2066", "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": ["Differential analysis was conducted using the R language limma package with |logFC| > 1 and p < 0.05 as the screening criteria."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}