Identification of necroptosis-related gene expression and the immune response in polycystic ovary syndrome.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39397125", "kind": "science-record", "revision": 3, "content_hash": "sha256:0ee8df66323e4537ac8c3e14ade7777f236a9374d8cf86a1c5af97671fe0191b", "created_at": "2026-11-01T20:29:37Z", "updated_at": "2026-11-01T22:12:54Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of necroptosis-related gene expression and the immune response in polycystic ovary syndrome.", "doi": "10.1007/s10815-024-03286-4", "pmid": "39397125", "authors": ["Xiuqin Tang", "Jinghua Ji", "Lili Zhu", "Fei Sun", "Lihong Wang", "Wenting Xu"], "journal": "Journal of assisted reproduction and genetics", "year": 2024, "abstract": "BACKGROUND: Polycystic ovary syndrome (PCOS) is a common reproductive and endocrine disorder; however, the understanding of the pathogenesis of PCOS remains unclear. Necroptosis is a newly discovered mechanism of cell death, and it is closely related to reproductive endocrine-related diseases. This study aimed to investigate the hub necroptosis-related genes in PCOS patients and its correlation with immune cell infiltration by bioinformatics methods.\nMETHOD: The gene expression chip result matrix and the annotation matrix files of the GSE34526, GSE8157, and GSE5090 datasets were downloaded from the GEO database. We analyzed the expression and correlation of the necroptosis-related genes in all samples, constructed a diagnostic model based on all necroptosis-related genes and genes with significant differences, performed unsupervised clustering of samples and gene enrichment analysis, and evaluated the correlations between the hub gene and immune cell infiltration levels by the R packages GSVA and CIBERSORT. Finally, PPI networks were constructed using the Cytoscape software GeneMANIA plug-in, and the miRNA, transcription factors, RBP, and drugs were predicted.\nCONCLUSION: Necroptosis-related genes have important relationships in the development of PCOS and are potentially associated with immune infiltration in PCOS patients.", "claims": [{"id": "claim-method", "statement": "Finally, Pearson’s correlation analysis was performed using the merged data set, and correlation analysis results were illustrated by constructing a correlation heat map (Fig. 2E).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39397125", "locator": "sections[4] \"Expression and correlation analysis of necroptosis-related genes in polycystic ovary syndrome\" paragraph 2", "quote": "Finally, Pearson’s correlation analysis was performed using the merged data set, and correlation analysis results were illustrated by constructing a correlation heat map (Fig. 2E)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data for this article come from public databases and are available for download. The gene expression chip result matrix and the annotation matrix files of the GSE34526, GSE8157, and GSE5090 datasets were downloaded from the GEO database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39397125", "locator": "sections[26] \"notes\" paragraph 1", "quote": "The data for this article come from public databases and are available for download. The gene expression chip result matrix and the annotation matrix files of the GSE34526, GSE8157, and GSE5090 datasets were downloaded from the GEO database."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Necroptosis-related genes have important relationships in the development of PCOS and are potentially associated with immune infiltration in PCOS patients.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39397125", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Necroptosis-related genes have important relationships in the development of PCOS and are potentially associated with immune infiltration in PCOS patients."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Necroptosis-related genes have important relationships in the development of PCOS and are potentially associated with immune infiltration in PCOS patients.", "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:39397125"], "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:GSE34526"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:student_t", "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:GSE34526"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:student_t"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39397125", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1007/s10815-024-03286-4", "sha256": "sha256:1706a4422339450fd70d886040fcb38e635aeb152a0850071e4b7b9bbfae5034", "bytes": 49328, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1007/s10815-024-03286-4", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11707095", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE34526", "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=GSE34526", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE34526", "version": null, "note": "The data for this article come from public databases and are available for download. The gene expression chip result matrix and the annotation matrix files of the GSE34526, GSE8157, and GSE5090 datasets were downloaded from the GEO database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data for this article come from public databases and are available for download. The gene expression chip result matrix and the annotation matrix files of the GSE34526, GSE8157, and GSE5090 datasets were downloaded from the GEO database.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM850527", "GSM850528", "GSM850529", "GSM850530", "GSM850531", "GSM850532", "GSM850533", "GSM850534", "GSM850535", "GSM850536"], "sample_count": 10, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Differential Gene Expression in Granulosa Cells from Polycystic Ovary Syndrome Patients with and without Insulin Resistance:  Identification of Susceptibility Gene Sets through Network Analysis", "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:GSE5090", "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=GSE5090", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE5090", "version": null, "note": "The data for this article come from public databases and are available for download. The gene expression chip result matrix and the annotation matrix files of the GSE34526, GSE8157, and GSE5090 datasets were downloaded from the GEO database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data for this article come from public databases and are available for download. 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