Identification of key genes related to heart failure by analysis of expression profiles.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38757035", "kind": "science-record", "revision": 4, "content_hash": "sha256:041d724cf5eaf7cfa646c9f59f066ed779ec02719bfe64d77b8b86a487099430", "created_at": "2026-11-01T19:20:43Z", "updated_at": "2026-11-01T22:54:19Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of key genes related to heart failure by analysis of expression profiles.", "doi": "10.5114/aoms/114896", "pmid": "38757035", "authors": ["Che Wang", "Qingmin Li", "Honghui Yang", "Chuanyu Gao", "Qiubo Du", "Caili Zhang", "Lijie Zhu", "Qingman Li"], "journal": "Archives of medical science : AMS", "year": 2024, "abstract": "Introduction: To elucidate the candidate biomarkers involved in the pathogenesis process of heart failure (HF) via analysis of differentially expressed genes (DEGs) of the dataset from the Gene Expression Omnibus (GEO).\nMaterial and methods: The GSE76701 gene expression profiles regarding the HF and control subjects were respectively analysed. Briefly, DEGs were firstly identified and subjected to Cytoscape plug-in ClueGO + CluePedia and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. A protein-protein interaction (PPI) network was then built to analyse the interaction between DEGs, followed by the construction of an interaction network by combining with hub genes with the targeted miRNA genes of DEGs to identify the key molecules of HF. In addition, potential drugs targeting key DEGs were sought using the drug-gene interaction database (DGIdb), and a drug-mRNA-miRNA interaction network was also constructed.\nResults: A total of 489 DEGs were verified between HF and control, which mainly enriched in type I interferon and leukocyte migration according to molecular function. Significantly increased levels of GAPDH, GALM1, MMP9, CCL5, and GNAL2 were found in the HF setting and were identified as the hub genes based on the PPI network. Furthermore, according to the drug-mRNA-miRNA network, FCGR2B, CCND1, and NF-κb, as well as corresponding miRNA-605-5p, miRNA-147a, and miRNA-671-5p were identified as the drug targets of HF.\nConclusions: The hub genes GAPDH, GALM1, MMP9, CCL5, and GNAL2 were significantly increased in HF. miRNA-605-5p, miRNA-147a, and miRNA-671-5p were predicted as the drug target-interacted gene-miRNA of HF.", "claims": [{"id": "claim-method", "statement": "For DEGs between HF and control, the p-value and logarithmic fold change (log2FC) were calculated using a freely available limma package (http://bioconductor.org/packages/release/bioc/html/limma.html, version 3.26.9) [17]. DEGs were determined by the threshold of p-value < 0.05 and |log2FC| > 0.585.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38757035", "locator": "sections[4] \"Screening of differentially expressed genes\" paragraph 2", "quote": "For DEGs between HF and control, the p-value and logarithmic fold change (log2FC) were calculated using a freely available limma package (http://bioconductor.org/packages/release/bioc/html/limma.html, version 3.26.9) [17]. DEGs were determined by the threshold of p-value < 0.05 and |log2FC| > 0.585."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Gene profiles of GSE76701 [16] were obtained from the National Centre of Biotechnology Information (NCBI) Gene Expression Omnibus database (GEO). GSE76701 was processed on Affymetrix Human Genome U133 Plus 2.0 Array (GPL570). GSE76701 contained 4 HF and 4 normal controls, and the mRNA was isolated from left ventricular tissue for microarray analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38757035", "locator": "sections[3] \"Data sources and preprocessing\" paragraph 2", "quote": "Gene profiles of GSE76701 [16] were obtained from the National Centre of Biotechnology Information (NCBI) Gene Expression Omnibus database (GEO). GSE76701 was processed on Affymetrix Human Genome U133 Plus 2.0 Array (GPL570). GSE76701 contained 4 HF and 4 normal controls, and the mRNA was isolated from left ventricular tissue for microarray analysis."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified 489 differentially expressed genes between heart failure and control samples, including 271 upregulated and 218 downregulated genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38757035", "locator": "sections[11] \"Identification of differentially expressed genes\" paragraph 2", "quote": "There were 489 DEGs in GSE76701, including 271 up- and 218 down-regulated genes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified 489 differentially expressed genes between heart failure and control samples, including 271 upregulated and 218 downregulated 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:38757035"], "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:GSE76701"], "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:GSE76701"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38757035", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.5114/aoms/114896", "sha256": "sha256:ee4d403aa28136e77f9c2b20cb2f0a14bd0609cc551ea99d3b1df87f14dd54cd", "bytes": 33683, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.5114/aoms/114896", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11094840", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE76701", "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=GSE76701", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE76701", "version": null, "note": "Gene profiles of GSE76701 [16] were obtained from the National Centre of Biotechnology Information (NCBI) Gene Expression Omnibus database (GEO). 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