Comparison of critical biomarkers in 2 erectile dysfunction models based on GEO and NOS-cGMP-PDE5 pathway.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34731136", "kind": "science-record", "revision": 4, "content_hash": "sha256:ef268e3564f7901ce626aceb59fcd737a4231652b20002710567baafc89032f8", "created_at": "2026-11-01T17:36:24Z", "updated_at": "2026-11-01T22:05:04Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comparison of critical biomarkers in 2 erectile dysfunction models based on GEO and NOS-cGMP-PDE5 pathway.", "doi": "10.1097/MD.0000000000027508", "pmid": "34731136", "authors": ["Guangying Wang", "Dayue Shen", "Xilan Zhang", "Monica G Ferrini", "Yuanping Li", "Hui Liao"], "journal": "Medicine", "year": 2021, "abstract": "BACKGROUND: Erectile dysfunction is a disease commonly caused by diabetes mellitus (DMED) and cavernous nerve injury (CNIED). Bioinformatics analyses including differentially expressed genes (DEGs), enriched functions and pathways (EFPs), and protein-protein interaction (PPI) networks were carried out in DMED and CNIED rats in this study. The critical biomarkers that may intervene in nitric oxide synthase (NOS, predominantly nNOS, ancillary eNOS, and iNOS)-cyclic guanosine monophosphate (cGMP)-phosphodiesterase 5 enzyme (PDE5) pathway, an important mechanism in erectile dysfunction treatment, were then explored for potential clinical applications.\nMETHODS: GSE2457 and GSE31247 were downloaded. Their DEGs with a |logFC (fold change)| > 0 were screened out. Database for Annotation, Visualization and Integrated Discovery (DAVID) online database was used to analyze the EFPs in Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes networks based on down-regulated and up-regulated DEGs respectively. PPI analysis of 2 datasets was performed in Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) and Cytoscape. Interactions with an average score greater than 0.9 were chosen as the cutoff for statistical significance.\nRESULTS: From a total of 1710 DEGs in GSE2457, 772 were down-regulated and 938 were up-regulated, in contrast to the 836 DEGs in GSE31247, from which 508 were down-regulated and 328 were up-regulated. The 25 common EFPs such as aging and response to hormone were identified in both models. PPI results showed that the first 10 hub genes in DMED were all different from those in CNIED.\nCONCLUSIONS: The intervention of iNOS with the hub gene complement component 3 in DMED and the aging process in both DMED and CNIED deserves attention.", "claims": [{"id": "claim-method", "statement": "The DEGs in the ED and non-ED specimen were picked out from GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r), which is a platform for examining DEGs across experimental conditions by comparing multiple datasets in GEO series. The genes with a |logFC (fold change)| > 0 and P < .05 were screened out and P < .05 represented statistical significance.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34731136", "locator": "sections[4] \"Identification of DEGs\" paragraph 2", "quote": "The DEGs in the ED and non-ED specimen were picked out from GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r), which is a platform for examining DEGs across experimental conditions by comparing multiple datasets in GEO series."}, {"asset": "source:pmid:34731136", "locator": "sections[4] \"Identification of DEGs\" paragraph 2", "quote": "The genes with a |logFC (fold change)| > 0 and P < .05 were screened out and P < .05 represented statistical significance."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Raw data is available at NCBI GEO: GSE2457 and GSE31247.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34731136", "locator": "sections[19] \"Footnotes\" paragraph 2", "quote": "Raw data is available at NCBI GEO: GSE2457 and GSE31247."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study used GEO2R to compare GSE2457 and GSE31247 with their respective non-ED controls and screened genes with |logFC (fold change)| > 0 and P < .05 as differentially expressed genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34731136", "locator": "sections[4] \"Identification of DEGs\" paragraph 2", "quote": "The DEGs in the ED and non-ED specimen were picked out from GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r), which is a platform for examining DEGs across experimental conditions by comparing multiple datasets in GEO series."}, {"asset": "source:pmid:34731136", "locator": "sections[4] \"Identification of DEGs\" paragraph 2", "quote": "The genes with a |logFC (fold change)| > 0 and P < .05 were screened out and P < .05 represented statistical significance."}, {"asset": "source:pmid:34731136", "locator": "sections[3] \"Microarray data\" paragraph 2", "quote": "Two gene expression datasets, namely GSE2457 entitled “Transcription profiling of rat penis samples from animals with diabetes-induced erectile dysfunction” and GSE31247 entitled “Gene expression profile on the penile tissue of erectile dysfunction (ED) in cavernous nerve injury (CNI) rat model”, were downloaded from GEO"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study used GEO2R to compare GSE2457 and GSE31247 with their respective non-ED controls and screened genes with |logFC (fold change)| > 0 and P < .05 as differentially expressed genes.", "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:34731136"], "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:GSE2457"], "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:GSE2457"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34731136", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1097/MD.0000000000027508", "sha256": "sha256:88c7dcdd6b1e81f3e749c948ea481ca1cd5d59c81592645a5938b320aece9f1e", "bytes": 46200, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1097/MD.0000000000027508", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8519209", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE2457", "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=GSE2457", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE2457", "version": null, "note": "Raw data is available at NCBI GEO: GSE2457 and GSE31247.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Raw data is available at NCBI GEO: GSE2457 and GSE31247.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM46500", "GSM46503", "GSM46508", "GSM46512", "GSM46516", "GSM46518", "GSM46519", "GSM46520", "GSM46521", "GSM46522"], "sample_count": 10, "group_sizes": null, "group_sizes_basis": null, "platform": "341", "taxon": "Rattus norvegicus", "title": "Control vs Diabetic Penile Tissues", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE31247", "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=GSE31247", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE31247", "version": null, "note": "Raw data is available at NCBI GEO: GSE2457 and GSE31247.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Raw data is available at NCBI GEO: GSE2457 and GSE31247.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM774597", "GSM774598", "GSM774599", "GSM774600", "GSM774601", "GSM774602"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "7289", "taxon": "Rattus norvegicus", "title": "Gene expression profile on the penile tissue of erectile dysfunction (ED)  in cavernous nerve injury (CNI) RAT model", "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:GSE2457 not downloaded", "asset:data:geo:GSE2457 licence not read", "asset:data:geo:GSE31247 not downloaded", "asset:data:geo:GSE31247 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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-2", "family": null, "specific": null, "label": "GEO2R comparison of ED and non-ED specimens, with DEGs selected using |logFC (fold change)| > 0 and P < .05.", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "reordered", "quote": "The DEGs in the ED and non-ED specimen were picked out from GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r), which is a platform for examining DEGs across experimental conditions by comparing multiple datasets in GEO series. The genes with a |logFC (fold change)| > 0 and P < .05 were screened out and P < .05 represented statistical significance."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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