Identification of co-expressed central genes and transcription factors in acute myocardial infarction and diabetic nephropathy.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38764052", "kind": "science-record", "revision": 4, "content_hash": "sha256:d439977cee19c0dccbbece60d5cac4daa8f939fbf54dd97cbb8ac795862f86af", "created_at": "2026-11-01T19:20:43Z", "updated_at": "2026-11-01T22:54:20Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of co-expressed central genes and transcription factors in acute myocardial infarction and diabetic nephropathy.", "doi": "10.1186/s12920-024-01906-7", "pmid": "38764052", "authors": ["Bo Li", "Xu Zhao", "Wanrun Xie", "Zhenzhen Hong", "Ye Cao", "Yi Zhang", "Yan Ding"], "journal": "BMC medical genomics", "year": 2024, "abstract": "BACKGROUND: Acute myocardial infarction (AMI) and diabetic nephropathy (DN) are common clinical co-morbidities, but they are challenging to manage and have poor prognoses. There is no research on the bioinformatics mechanisms of comorbidity, and this study aims to investigate such mechanisms.\nMETHODS: We downloaded the AMI data (GSE66360) and DN datasets (GSE30528 and GSE30529) from the Gene Expression Omnibus (GEO) platform. The GSE66360 dataset was divided into two parts: the training set and the validation set, and GSE30529 was used as the training set and GSE30528 as the validation set. After identifying the common differentially expressed genes (DEGs) in AMI and DN in the training set, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses and protein-protein interaction (PPI) network construction were performed. A sub-network graph was constructed by MCODE, and 15 hub genes were screened by the Cytohubba plugin. The screened hub genes were validated, and the 15 screened hub genes were subjected to GO, KEGG, Gene MANIA analysis, and transcription factor (TF) prediction. Finally, we performed TF differential analysis, enrichment analysis, and TF and gene regulatory network construction.\nRESULTS: A total of 46 genes (43 up-regulated and 3 down-regulated) were identified for subsequent analysis. GO functional analysis emphasized the presence of genes mainly in the vesicle membrane and secretory granule membrane involved in antigen processing and presentation, lipopeptide binding, NAD + nucleosidase activity, and Toll-like receptor binding. The KEGG pathways analyzed were mainly in the phagosome, neutrophil extracellular trap formation, natural killer cell-mediated cytotoxicity, apoptosis, Fc gamma R-mediated phagocytosis, and Toll-like receptor signaling pathways. Eight co-expressed hub genes were identified and validated, namely TLR2, FCER1G, CD163, CTSS, CLEC4A, IGSF6, NCF2, and MS4A6A. Three transcription factors were identified and validated in AMI, namely NFKB1, HIF1A, and SPI1.\nCONCLUSIONS: Our study reveals the common pathogenesis of AMI and DN. These common pathways and hub genes may provide new ideas for further mechanistic studies.", "claims": [{"id": "claim-method", "statement": "We cleaned the data, removed the probes without gene annotation, averaged the duplicate probes, normalized and log2-transformed the data, and performed difference analysis for the GSE66360 training set and GSE30529 using the \"limma\" R package [13].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38764052", "locator": "sections[4] \"Differentially expressed genes\" paragraph 2", "quote": "We cleaned the data, removed the probes without gene annotation, averaged the duplicate probes, normalized and log2-transformed the data, and performed difference analysis for the GSE66360 training set and GSE30529 using the \"limma\" R package [13]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The current dataset analyzed in the study can be found in the GEO database.\nGSE66360: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE66360.\nGSE30528: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30528.\nGSE30529: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30529.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38764052", "locator": "sections[28] \"Availability of data and materials\" paragraphs 1-5", "quote": "The current dataset analyzed in the study can be found in the GEO database.\nGSE66360: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE66360.\nGSE30528: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30528.\nGSE30529: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30529."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Eight co-expressed hub genes were identified and validated, namely TLR2, FCER1G, CD163, CTSS, CLEC4A, IGSF6, NCF2, and MS4A6A.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38764052", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Eight co-expressed hub genes were identified and validated, namely TLR2, FCER1G, CD163, CTSS, CLEC4A, IGSF6, NCF2, and MS4A6A."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Eight co-expressed hub genes were identified and validated, namely TLR2, FCER1G, CD163, CTSS, CLEC4A, IGSF6, NCF2, and MS4A6A.", "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:38764052"], "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:GSE30528"], "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:GSE30528"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38764052", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12920-024-01906-7", "sha256": 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