Integrated bioinformatics analysis identifies hub genes and immune regulatory networks in HIV infection.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40574839", "kind": "science-record", "revision": 4, "content_hash": "sha256:c2d63a3bb299554f9763e29f03fe0c0f15ba3a6066d72926841934ac7a4ef89b", "created_at": "2026-11-01T20:30:39Z", "updated_at": "2026-11-01T22:56:42Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated bioinformatics analysis identifies hub genes and immune regulatory networks in HIV infection.", "doi": "10.3389/fimmu.2025.1600713", "pmid": "40574839", "authors": ["Xiaoxia Pang", "Xinghong Chen", "Yuxin Jing", "Feng Shi", "Xiaoying Chen", "Huatuo Huang", "Chunhong Liu"], "journal": "Frontiers in immunology", "year": 2025, "abstract": "Introduction: Acquired Immune Deficiency Syndrome (AIDS) is a chronic and life-threatening condition caused by the human immunodeficiency virus (HIV), which severely weakens the immune system. Despite advances in treatment, AIDS remains incurable. Understanding the molecular mechanisms underlying AIDS progression is crucial for developing effective therapeutic strategies. Therefore, this study aims to identify hub genes associated with AIDS susceptibility and progression, as well as to elucidate potential molecular mechanisms involved.\nMethods: We used the Gene Expression Omnibus (GEO) dataset GSE76246 for this study. Differentially expressed genes (DEGs) were screened, and Weighted Gene Co-expression Network Analysis (WGCNA) was employed to construct gene modules associated with HIV infection. Hub genes were identified using the CytoHubba plugin, and their expression profiles were assessed using box plots. The diagnostic potential of these genes was evaluated using receiver operating characteristic (ROC) analysis. Functional enrichment and Gene Set Enrichment Analysis (GSEA) were conducted to identify key biological pathways. Additionally, we analyzed immune cell infiltration and constructed drug-gene interaction, miRNA and transcription factor (TF) regulatory networks.\nResults: 101 intersection genes were identified by combining DEGs, Oxidative stress genes and module genes from WGCNA. Functional enrichment analysis highlighted key pathways, including oxidative stress response and apoptotic signaling. A protein-protein interaction (PPI) network analysis identified 10 hub genes (TP53, AKT1, JUN, CTNNB1, PXDN, MAPK3, FOS, MMP9, FOXO1, STAT1), which showed strong diagnostic potential, as evidenced by ROC curve analysis. Immune infiltration analysis revealed significant associations between hub genes and various immune cell populations. Furthermore, drug-gene interaction analysis predicted several potential therapeutic compounds. Additionally, miRNA and TF regulatory networks were constructed, identifying critical regulatory elements influencing the expression of hub genes.\nConclusion: This study identified ten hub genes (TP53, AKT1, JUN, CTNNB1, PXDN, MAPK3, FOS, MMP9, FOXO1, STAT1) that play crucial roles in HIV infection and progression. These genes serve as potential biomarkers for HIV diagnosis and therapeutic targets.", "claims": [{"id": "claim-method", "statement": "DEGs between 30 HIV-positive and 7 HIV-negative samples were identified using the R package limma.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40574839", "locator": "sections[4] \"Identification of DEGs\" paragraph 2", "quote": "DEGs between 30 HIV-positive and 7 HIV-negative samples were identified using the R package limma."}], "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:40574839", "locator": "sections[28] \"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 study identified ten hub genes associated with HIV infection and progression using the GSE76246 dataset through differential-expression, WGCNA, functional-enrichment, PPI-network, and ROC analyses.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40574839", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "This study identified ten hub genes (TP53, AKT1, JUN, CTNNB1, PXDN, MAPK3, FOS, MMP9, FOXO1, STAT1) that play crucial roles in HIV infection and progression."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified ten hub genes associated with HIV infection and progression using the GSE76246 dataset through differential-expression, WGCNA, functional-enrichment, PPI-network, and ROC analyses.", "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:40574839"], "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:GSE76246"], "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:GSE76246"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40574839", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fimmu.2025.1600713", "sha256": "sha256:140839fa36b2c443da42302f731e206598b839f2fdb4ded50e8c0b764cc2bcaa", "bytes": 63054, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fimmu.2025.1600713", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12197935", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE76246", "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=GSE76246", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE76246", "version": null, "note": "The datasets presented in this study can be found in online repositories. 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