Left ventricular assist device bioinformatics identify possible hubgenes and regulatory networks involved in the myocardium of patients with left ventricular assist device.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36247468", "kind": "science-record", "revision": 4, "content_hash": "sha256:1715cf84dae97ab574e0042156ed10800d345aa029c721e44dc860ec5d4d57b8", "created_at": "2026-11-01T18:15:38Z", "updated_at": "2026-11-01T22:07:52Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Left ventricular assist device bioinformatics identify possible hubgenes and regulatory networks involved in the myocardium of patients with left ventricular assist device.", "doi": "10.3389/fcvm.2022.912760", "pmid": "36247468", "authors": ["Maryam Ajmal", "Aisha Ajmal", "Maryam Rizvi", "Umar Salim", "Lei Huang"], "journal": "Frontiers in cardiovascular medicine", "year": 2022, "abstract": "Objective: The aim of this study was to clarify the changes of myocardial gene expression profile after left ventricular assist device (LVAD) implantation and the related molecular biological significance.\nMethods: A thorough bioinformatic analysis to evaluate the changes in gene expression profile in patients pre-LVAD and post-LVAD was conducted. Four relevant gene expression datasets-GSE430, GSE974, GSE21610, and GSE52601 from Gene Expression Omnibus (GEO) database were downloaded. Analysis of GEO2R, Gene Ontology (GO), protein-protein interaction (PPI) were used to determine differentially expressed genes (DEGs) and their function, respectively.\nResults: A total of 37 DEGs were identified, including 26 down-regulated and 11 up-regulated genes. The molecular function of DEGs were enriched in \"cytokine activity,\" \"neurotransmitter binding,\" \"receptor ligand activity.\" The gene set enrichment analysis (GSEA) revealed an overall marked increase of neutrophil degranulation signaling, closely correlated with the G protein coupled receptor (GPCR)-ligand binding process after LVAD assistance. 16 hubgenes in these DEGs were further selected and the biological process involved is mainly related to positive regulation of leukocyte chemotaxis mediated by chemokines.\nConclusion: Inflammatory signaling pathway is crucial for the pathophysiology after LVAD implantation. Chemokines mediate cardiac inflammatory response and tissue remodeling after LVAD implantation through GPCR-ligand binding.", "claims": [{"id": "claim-method", "statement": "To identify genes that are differently expressed in cardiac tissue between pre and post-LVAD treatment, the raw transcriptome data from the four datasets acquired from the GEO database were processed using the web tool GEO2R.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36247468", "locator": "sections[4] \"Data processing and differently expressed gene identification\" paragraph 2", "quote": "To identify genes that are differently expressed in cardiac tissue between pre and post-LVAD treatment, the raw transcriptome data from the four datasets acquired from the GEO database were processed using the web tool GEO2R."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. This data can be found here: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE430; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE974; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21610; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52601.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36247468", "locator": "sections[18] \"Data availability statement\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. This data can be found here: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE430; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE974; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21610; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52601."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified 37 differentially expressed genes after LVAD implantation, including 26 down-regulated and 11 up-regulated genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36247468", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 37 DEGs were identified, including 26 down-regulated and 11 up-regulated genes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified 37 differentially expressed genes after LVAD implantation, including 26 down-regulated and 11 up-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:36247468"], "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:GSE21610"], "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:GSE21610"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36247468", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fcvm.2022.912760", "sha256": "sha256:a1d2f5d6b7dc1c4d3b3b8507e1ac5d1a0149edf57cc2957385b0edb323dcb2b5", "bytes": 31225, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fcvm.2022.912760", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9558819", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE21610", "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=GSE21610", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE21610", "version": null, "note": "Publicly available datasets were analyzed in this study. 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