A combination analysis based on bioinformatics tools reveals new signature genes related to maternal obesity and fetal programming.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39296904", "kind": "science-record", "revision": 4, "content_hash": "sha256:99e40629b08147acc28325d377c3484e006a8d54336eebe03486e8f85710a9b6", "created_at": "2026-11-01T20:29:28Z", "updated_at": "2026-11-01T22:55:13Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A combination analysis based on bioinformatics tools reveals new signature genes related to maternal obesity and fetal programming.", "doi": "10.3389/fmed.2024.1434105", "pmid": "39296904", "authors": ["Chunhong Liu", "Yulan Lu", "Chunchuan Huang", "Yonglong Zeng", "Yuye Zheng", "Chunfang Wang", "Huatuo Huang"], "journal": "Frontiers in medicine", "year": 2024, "abstract": "Background: Maternal obesity significantly influences fetal development and health later in life; however, the molecular mechanisms behind it remain unclear. This study aims to investigate signature genes related to maternal obesity and fetal programming based on a genomic-wide transcriptional placental study using a combination of different bioinformatics tools.\nMethods: The dataset (GSE128381) was obtained from Gene Expression Omnibus (GEO). The data of 100 normal body mass index (BMI) and 27 obese mothers were included in the analysis. Differentially expressed genes (DEGs) were evaluated by limma package. Thereafter, functional enrichment analysis was implemented. Then, weighted gene co-expression network analysis (WGCNA) and the least absolute shrinkage and selection operator (LASSO) analysis were used to further screening of signature genes. Simple linear regression analysis was used to assess the correlation between signature genes and newborn birth weight. Gene set enrichment analysis (GSEA) was implemented to study signaling pathways related to signature genes. The expression of the signature genes was also explored in 48 overweight mothers in the same dataset.\nResults: A total of 167 DEGs were obtained, of which 122 were up-regulated while 45 were down-regulated. The dataset was then clustered into 11 modules by WGCNA, and the MEbrown was found as the most significant module related to maternal obesity and fetal programming (cor = 0.2, p = 0.03). The LASSO analysis showed that PTX3, NCF2, HOXB5, ABCA6, and C1orf162 are signature genes related to maternal obesity and fetal programming, which were increased in the placenta of obese mothers compared to those with normal BMI. The area under the curve (AUC) of the signature genes in the receiver operating characteristic curve (ROC) was 0.709, 0.660, 0.674, 0.667, and 0.717, respectively. Simple linear regression analysis showed that HOXB5 was associated with newborn birth weight. GSEA analysis revealed that these signature genes positively participate in various signaling pathways/functions in the placenta.\nConclusion: PTX3, NCF2, HOXB5, ABCA6, and C1orf162 are novel signature genes related to maternal obesity and fetal programming, of which HOXB5 is implicated in newborn birth weight.", "claims": [{"id": "claim-method", "statement": "The DEGs between mothers with obesity and normal pregnancy were screened using limma package (11), with criteria as listed below: p-value less than 0.05 and log | Fold change (FC)| larger than 0.3.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39296904", "locator": "sections[4] \"Identification of DEGs\" paragraph 2", "quote": "The DEGs between mothers with obesity and normal pregnancy were screened using limma package (11), with criteria as listed below: p-value less than 0.05 and log | Fold change (FC)| larger than 0.3."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary material.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39296904", "locator": "sections[23] \"Data availability statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary material."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The limma analysis identified 167 differentially expressed genes between obese and normal-BMI placentas, comprising 122 up-regulated and 45 down-regulated genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39296904", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 167 DEGs were obtained, of which 122 were up-regulated while 45 were down-regulated."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The limma analysis identified 167 differentially expressed genes between obese and normal-BMI placentas, comprising 122 up-regulated and 45 down-regulated 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:39296904"], "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:GSE128381"], "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:GSE128381"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39296904", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fmed.2024.1434105", "sha256": "sha256:fd4882506bf47bdbf72c9b3beeb6ceb91f1780471ac740a16044d7f10b629923", "bytes": 30787, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fmed.2024.1434105", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11408335", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE128381", "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=GSE128381", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE128381", "version": null, "note": "The datasets presented in this study can be found in online repositories. 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