Regulatory network analysis based on integrated miRNA-TF reveals key genes in heart failure.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38886500", "kind": "science-record", "revision": 4, "content_hash": "sha256:95263f9f55c173e0846dec8b5db753f498b1dcc187f4c4bedc288ca6634e4889", "created_at": "2026-11-01T20:28:57Z", "updated_at": "2026-11-01T22:54:30Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Regulatory network analysis based on integrated miRNA-TF reveals key genes in heart failure.", "doi": "10.1038/s41598-024-64732-y", "pmid": "38886500", "authors": ["Ziyue Zhang", "Ziying Zou", "Hui Zhang", "Dai-Min Zhang"], "journal": "Scientific reports", "year": 2024, "abstract": "The etiology and pathophysiology of heart failure are still unknown. Increasing evidence suggests that abnormal microRNAs (miRNAs) and transcription factors (TFs) expression may be associated with the development of heart failure. Therefore, this study aims to explore key miRNAs, TFs, and related genes in heart failure to gain a greater understanding of the pathogenesis of heart failure. To search and download the dataset of mRNA chips related to heart failure from the GEO database (GSE59867, GSE9128, and GSE134766), we analyzed differential genes and screened the common differentially expressed genes on two chips using R language software. The binary interactions and circuits among miRNAs, TFs, and corresponding genes were determined by Pearson correlation coefficient. A regulatory network of miRNAs, TFs, and target genes was constructed based on bioinformatics. By comparing the sequences of patients with and without heart failure, five downregulated genes with hypermethylated mRNA and three upregulated genes with hypomethylated mRNA were identified. The miRNA-TF gene regulatory network consisted of 26 miRNAs, 22 TFs and six genes. GO and KEGG analysis results revealed that BP terms like cellular response to organic substance, cellular response to cytokine stimulus, and KEGG pathways like osteoclast differentiation, MAPK signaling pathway, and legionellosis were enriched of the DEGs. TMEM87A, PPP2R2A, DUSP1, and miR-92a have great potential as biomarkers for heart failure. The integrated analysis of the mRNA expression spectrum and microRNA-transcription factor-gene revealed the regulatory network of heart failure, which may provide clues to its alternative treatment.", "claims": [{"id": "claim-method", "statement": "The empirical Bayes method in limma package was used to screen DEGs with the screening threshold as the corrected P-value < 0.05 and | logFC |≥ 1.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38886500", "locator": "sections[5] \"Screening of differentially expressed genes (DEGs)\" paragraph 2", "quote": "The empirical Bayes method in limma package was used to screen DEGs with the screening threshold as the corrected P-value < 0.05 and | logFC |≥ 1."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. This data can be found here: Gene Expression Omnibus: GSE59867, GSE9128, GSE134766. Data is provided within the manuscript or supplementary information files.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38886500", "locator": "sections[25] \"notes\" paragraph 1", "quote": "Publicly available datasets were analyzed in this study. This data can be found here: Gene Expression Omnibus: GSE59867, GSE9128, GSE134766. Data is provided within the manuscript or supplementary information files."}], "state": "complete"}, {"id": "claim-target-result", "statement": "TMEM87A, PPP2R2A, DUSP1, and miR-92a have great potential as biomarkers for heart failure.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38886500", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "TMEM87A, PPP2R2A, DUSP1, and miR-92a have great potential as biomarkers for heart failure."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "TMEM87A, PPP2R2A, DUSP1, and miR-92a have great potential as biomarkers for heart failure.", "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:38886500"], "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. 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