Identification of hub genes, diagnostic model, and immune infiltration in preeclampsia by integrated bioinformatics analysis and machine learning.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39709373", "kind": "science-record", "revision": 3, "content_hash": "sha256:e48f6593ad2a08a8c4026e1bab950c0a5c0ce757f3fec36e3f5e759d36d09d2b", "created_at": "2026-11-01T20:30:01Z", "updated_at": "2026-11-01T22:13:24Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of hub genes, diagnostic model, and immune infiltration in preeclampsia by integrated bioinformatics analysis and machine learning.", "doi": "10.1186/s12884-024-07028-3", "pmid": "39709373", "authors": ["Yihan Zheng", "Zhuanji Fang", "Xizhu Wu", "Huale Zhang", "Pengming Sun"], "journal": "BMC pregnancy and childbirth", "year": 2024, "abstract": "PURPOSE: This study aimed to identify novel biomarkers for preeclampsia (PE) diagnosis by integrating Weighted Gene Co-expression Network Analysis (WGCNA) with machine learning techniques.\nPATIENTS AND METHODS: We obtained the PE dataset GSE25906 from the gene expression omnibus (GEO) database. Analysis of differentially expressed genes (DEGs) and module genes with Limma and Weighted Gene Co-expression Network analysis (WGCNA). Candidate hub genes for PE were identified using machine learning. Subsequently, we used western-blotting (WB) and real-time fluorescence quantitative (qPCR) to verify the expression of F13A1 and SCCPDH in preeclampsia patients. Finally, we estimated the extent of immune cell infiltration in PE samples by employing the CIBERSORT algorithms.\nRESULTS: Our findings revealed that F13A1 and SCCPDH were the hub genes of PE. The nomogram and two candidate hub genes had high diagnostic values (AUC: 0.90 and 0.88, respectively). The expression levels of F13A1 and SCCPDH were verified by WB and qPCR. CIBERSORT analysis confirmed that the PE group had a significantly larger proportion of plasma cells and activated dendritic cells and a lower portion of resting memory CD4 + T cells.\nCONCLUSION: The study proposes F13A1 and SCCPDH as potential biomarkers for diagnosing PE and points to an improvement in early detection. Integration of WGCNA with machine learning could enhance biomarker discovery in complex conditions like PE and offer a path toward more precise and reliable diagnostic tools.", "claims": [{"id": "claim-method", "statement": "The diagnostic value of the nomogram was evaluated using the receiver operating characteristic (ROC) curve.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39709373", "locator": "sections[11] \"Diagnostic model\" paragraph 2", "quote": "The diagnostic value of the nomogram was evaluated using the receiver operating characteristic (ROC) curve."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The PE dataset used in this study (GSE25906) was obtained from the Gene Expression Omnibus (GEO) database. This dataset included gene expression profiles of placental samples from PE patients (n = 23) and normal pregnant women (n = 37). (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA135777). The authors declare that all data needed to evaluate the conclusions in the paper are present in the supplementary materials. The data can be provided by Yihan Zheng pending scientific review and a completed material transfer agreement. Requests for the data should be submitted to: zyh@fjmu.edu.cn. The original, unprocessed Western blot images, are available in the Supplementary material in this manuscript submission.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39709373", "locator": "sections[40] \"notes\" paragraph 1", "quote": "The PE dataset used in this study (GSE25906) was obtained from the Gene Expression Omnibus (GEO) database. This dataset included gene expression profiles of placental samples from PE patients (n = 23) and normal pregnant women (n = 37). (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA135777). The authors declare that all data needed to evaluate the conclusions in the paper are present in the supplementary materials. The data can be provided by Yihan Zheng pending scientific review and a completed material transfer agreement. Requests for the data should be submitted to: zyh@fjmu.edu.cn. The original, unprocessed Western blot images, are available in the Supplementary material in this manuscript submission."}], "state": "complete"}, {"id": "claim-target-result", "statement": "F13A1 and SCCPDH showed high diagnostic values for preeclampsia, with AUCs of 0.90 and 0.88, respectively.", "kind": "quantitative", "target": {"value": 95.0, "unit": "per cent", "tolerance": null, "source": "The AUC and 95% CI were as follows: F13A1 (AUC: 0.90, 95% CI 0.82–0.98) and SCCPDH (AUC: 0.88, 95% CI: 0.79–0.97) (Fig. 7C, D)."}, "evidence": [{"asset": "source:pmid:39709373", "locator": "sections[25] \"Diagnostic value assessment\" paragraph 2", "quote": "The AUC and 95% CI were as follows: F13A1 (AUC: 0.90, 95% CI 0.82–0.98) and SCCPDH (AUC: 0.88, 95% CI: 0.79–0.97) (Fig. 7C, D)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "F13A1 and SCCPDH showed high diagnostic values for preeclampsia, with AUCs of 0.90 and 0.88, respectively.", "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:39709373"], "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:GSE25906"], "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:GSE25906"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39709373", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12884-024-07028-3", "sha256": "sha256:3c0bbba2583f80d74bdaef8a1fd835e7c528e9b4a3e6895d281232198e17eb42", "bytes": 39522, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12884-024-07028-3", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11662826", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE25906", "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=GSE25906", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE25906", "version": null, "note": "The PE dataset used in this study (GSE25906) was obtained from the Gene Expression Omnibus (GEO) database. This dataset included gene expression profiles of placental samples from PE patients (n = 23) and normal pregnant women (n = 37). (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA135777). The authors declare that all data needed to evaluate the conclusions in the paper are present in the supplementary materials. The data can be provided by Yihan Zheng pending scientific review and a completed material transfer agreement. Requests for the data should be submitted to: zyh@fjmu.edu.cn. The original, unprocessed Western blot images, are available in the Supplementary material in this manuscript submission.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The PE dataset used in this study (GSE25906) was obtained from the Gene Expression Omnibus (GEO) database. This dataset included gene expression profiles of placental samples from PE patients (n = 23) and normal pregnant women (n = 37). 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