Identification of Key Nucleotide Metabolism Genes in Diabetic Retinopathy Based on Bioinformatics Analysis and Experimental Verification.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40282274", "kind": "science-record", "revision": 4, "content_hash": "sha256:14c80462cd44c9860afa1f320631a26f50408fd1174ea0e519c29547e4beea46", "created_at": "2026-11-01T20:30:26Z", "updated_at": "2026-11-01T22:56:25Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Key Nucleotide Metabolism Genes in Diabetic Retinopathy Based on Bioinformatics Analysis and Experimental Verification.", "doi": "10.3390/biology14040409", "pmid": "40282274", "authors": ["Wei Wang", "Jianyang Gong"], "journal": "Biology", "year": 2025, "abstract": "A dysregulated nucleotide metabolism has been implicated in the pathogenesis of diabetic retinopathy (DR). RNA sequencing datasets, GSE102485, GSE60436, and GSE165784, were downloaded from the GEO database. The differentially expressed genes (DEGs) between the DR and controls overlapped with nucleotide metabolism-related genes (NM-RGs), resulting in the differentially expressed NM-RGs (DE-NMRGs). Next, the core genes were identified by the five algorithms of the CytoHubba plugin. Receiver Operating Characteristic (ROC) curves and gene expression analysis were utilized to confirm the biomarkers. Then, the correlations between biomarker expression and the immune-related module were analyzed. The miRNA and transcription factor (TF) predictions, biomarker-targeting drugs, and molecular docking were implemented separately. The interaction between each subcluster of DR was elucidated through single-cell RNA (scRNA) analysis. Moreover, RT-PCR was applied to verify the expression of the biomarkers. In GSE102485, 48 DE-NMRGs were identified via the intersection of 1359 DEGs and 882 NM-RGs. Using the CytoHubba plugin, HMOX1, TLR4, and ACE were selected as core genes. As per the GSVA result, the interferon alpha response, IL6_JAK_STAT3 signaling, and apoptosis were activated in the DR group. The TF prediction identified TLR4 and HMOX1 as potential target genes of USF2. In conclusion, ACE and HMOX1 were possible diagnostic biomarkers related to nucleotide metabolism in DR.", "claims": [{"id": "claim-method", "statement": "Within the GSE102485 dataset, we utilized the R package DESeq2 (v. 1.34.0) to identify DEGs between diabetic retinopathy and normal samples (|log2FC| > 0.5, p value < 0.05).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40282274", "locator": "sections[4] \"2.2. Identification of DEGs\" paragraph 2", "quote": "Within the GSE102485 dataset, we utilized the R package DESeq2 (v. 1.34.0) to identify DEGs between diabetic retinopathy and normal samples (|log2FC| > 0.5, p value < 0.05)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All the RNA-sequencing data of diabetic retinopathy patients were acquired from the Gene Expression Omnibus database (GEO, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi, (accessed on 20 November 2024)).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40282274", "locator": "sections[34] \"notes\" paragraph 1", "quote": "All the RNA-sequencing data of diabetic retinopathy patients were acquired from the Gene Expression Omnibus database (GEO, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi, (accessed on 20 November 2024))."}], "state": "complete"}, {"id": "claim-target-result", "statement": "In GSE102485, 48 DE-NMRGs were identified via the intersection of 1359 DEGs and 882 NM-RGs.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40282274", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "In GSE102485, 48 DE-NMRGs were identified via the intersection of 1359 DEGs and 882 NM-RGs."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "In GSE102485, 48 DE-NMRGs were identified via the intersection of 1359 DEGs and 882 NM-RGs.", "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:40282274"], "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:GSE102485"], "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:GSE102485"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40282274", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/biology14040409", "sha256": "sha256:9f8a0410abd3970525311962802f890b6b29bdeb8f1ec9be4d56f71bfff153d3", "bytes": 41516, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/biology14040409", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12024606", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE102485", "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=GSE102485", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE102485", "version": null, "note": "All the RNA-sequencing data of diabetic retinopathy patients were acquired from the Gene Expression Omnibus database (GEO, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi, (accessed on 20 November 2024)).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All the RNA-sequencing data of diabetic retinopathy patients were acquired from the Gene Expression Omnibus database (GEO, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi, (accessed on 20 November 2024)).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2739339", "GSM2739340", "GSM2739341", "GSM2739342", "GSM2739343", "GSM2739344", "GSM2739345", "GSM2739346", "GSM2739347", "GSM2739348", "GSM2739349", "GSM2739350", "GSM2739351", "GSM2739352", "GSM2739353", "GSM2739354", "GSM2739355", "GSM2739356", "GSM2739357", "GSM2739358", "GSM2739359", "GSM2739360", "GSM2739361", "GSM2739362", "GSM2739363", "GSM2739364", "GSM2739365", "GSM2739366", "GSM2739367", "GSM2739368"], "sample_count": 30, "group_sizes": null, "group_sizes_basis": null, "platform": "18573", "taxon": "Homo sapiens", "title": "Induced Expression of VEGFC, ANGPT, and EFNB2 and Their Receptors Characterizes Neovascularization in Proliferative Diabetic Retinopathy", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE165784", "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=GSE165784", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE165784", "version": null, "note": "All the RNA-sequencing data of diabetic retinopathy patients were acquired from the Gene Expression Omnibus database (GEO, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi, (accessed on 20 November 2024)).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All the RNA-sequencing data of diabetic retinopathy patients were acquired from the Gene Expression Omnibus database (GEO, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi, (accessed on 20 November 2024)).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM5049904", "GSM5049905", "GSM5049906", "GSM5277737", "GSM5690478", "GSM5690479"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "20795", "taxon": "Homo sapiens", "title": "Single-cell RNA-sequencing reveals the heterogeneity of microglia in fibrous membrane derived from proliferative diabetic retinopathy and proliferative vitreoretinopathy", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE60436", "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=GSE60436", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE60436", "version": null, "note": "All the RNA-sequencing data of diabetic retinopathy patients were acquired from the Gene Expression Omnibus database (GEO, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi, (accessed on 20 November 2024)).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All the RNA-sequencing data of diabetic retinopathy patients were acquired from the Gene Expression Omnibus database (GEO, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi, (accessed on 20 November 2024)).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1479904", "GSM1479905", "GSM1479906", "GSM1479907", "GSM1479908", "GSM1479909", "GSM1479910", "GSM1479911", "GSM1479912"], "sample_count": 9, "group_sizes": null, "group_sizes_basis": null, "platform": "6884", "taxon": "Homo sapiens", "title": "Gene Expression Profile of Fibrovascular Membrane Associated with Proliferative Diabetic Retinopathy", "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:GSE102485 not downloaded", "asset:data:geo:GSE102485 licence not read", "asset:data:geo:GSE165784 not downloaded", "asset:data:geo:GSE165784 licence not read", "asset:data:geo:GSE60436 not downloaded", "asset:data:geo:GSE60436 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "deseq2", "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": "Within the GSE102485 dataset, we utilized the R package DESeq2 (v. 1.34.0) to identify DEGs between diabetic retinopathy and normal samples (|log2FC| > 0.5, p value < 0.05)."}}, {"id": "method-2", "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"}}], "targets": [], "gaps": []}, "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: deseq2."}, "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": ["GSE102485", "GSE60436", "GSE165784"], "resolved_accessions": ["GSE102485", "GSE60436", "GSE165784"], "statements": ["All the RNA-sequencing data of diabetic retinopathy patients were acquired from the Gene Expression Omnibus database (GEO, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi, (accessed on 20 November 2024))."], "basis": "The paper names GSE102485, GSE60436, GSE165784 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:40282274", "data:geo:GSE102485"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE102485"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:51:02Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 11331, "completion_tokens": 1298, "cached_tokens": 128}}, "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:40282274", "type": "paper", "label": "pmid:40282274"}, {"id": "source:pmid:40282274", "type": "manuscript", "label": "PMID 40282274 full text"}, {"id": "data:geo:GSE102485", "type": "dataset", "label": "GEO GSE102485"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:40282274", "type": "paper", "label": "pmid:40282274"}, {"id": "source:pmid:40282274", "type": "manuscript", "label": "PMID 40282274 full text"}, {"id": "data:geo:GSE102485", "type": "dataset", "label": "GEO GSE102485"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-40282274", "type": "extraction", "used": ["source:pmid:40282274"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE102485", "type": "accession_resolution", "used": ["data:geo:GSE102485"], "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:40282274", "parent_hash": "sha256:4f1c58a71f6021d7a70605fec9ec4ef424691b9144d05319726170d183e98b3e", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE102485 licence not read", "asset:data:geo:GSE102485 not downloaded", "asset:data:geo:GSE165784 licence not read", "asset:data:geo:GSE165784 not downloaded", "asset:data:geo:GSE60436 licence not read", "asset:data:geo:GSE60436 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["e pathogenesis of diabetic retinopathy (DR). RNA sequencing datasets, GSE102485, GSE60436, and GSE165784"], "order_basis": "paper_text_order:200", "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": 0.69, "evidence": ["alpha response, IL6_JAK_STAT3 signaling, and apoptosis were activated in the DR group. The TF predi"], "order_basis": "paper_text_order:1353", "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": ["Within the GSE102485 dataset, we utilized the R package DESeq2 (v. 1.34.0) to identify DEGs between diabetic retinopathy and normal samples (|log2FC| > 0.5, p value < 0.05)."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}