Identification of Hub Genes in the Remodeling of Non-Infarcted Myocardium Following Acute Myocardial Infarction.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36547406", "kind": "science-record", "revision": 4, "content_hash": "sha256:eb78a3e22404c4c64666ad8565d2f6ec0e7de47b907fd0202924112f1f2b809b", "created_at": "2026-11-01T19:01:04Z", "updated_at": "2026-11-01T22:50:53Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Hub Genes in the Remodeling of Non-Infarcted Myocardium Following Acute Myocardial Infarction.", "doi": "10.3390/jcdd9120409", "pmid": "36547406", "authors": ["Lingxiao Wang", "Yan Zhang", "Mengjie Yu", "Wuzhou Yuan"], "journal": "Journal of cardiovascular development and disease", "year": 2022, "abstract": "(1) Background: There are few diagnostic and therapeutic targets for myocardial remodeling in the salvageable non-infarcted myocardium. (2) Methods: Hub genes were identified through comprehensive bioinformatics analysis (GSE775, GSE19322, and GSE110209 from the gene expression omnibus (GEO) database) and the biological functions of hub genes were examined by gene ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment. Furthermore, the differential expression of hub genes in various cell populations between the acute myocardial infarction (AMI) and sham-operation groups was analyzed by processing scRNA data (E-MTAB-7376 from the ArrayExpress database) and RNA-seq data (GSE183168). (3) Results: Ten strongly interlinked hub genes (Timp1, Sparc, Spp1, Tgfb1, Decr1, Vim, Serpine1, Serpina3n, Thbs2, and Vcan) were identified by the construction of a protein-protein interaction network from 135 differentially expressed genes identified through comprehensive bioinformatics analysis and their reliability was verified using GSE119857. In addition, the 10 hub genes were found to influence the ventricular remodeling of non-infarcted tissue by modulating the extracellular matrix (ECM)-mediated myocardial fibrosis, macrophage-driven inflammation, and fatty acid metabolism. (4) Conclusions: Ten hub genes were identified, which may provide novel potential targets for the improvement and treatment of AMI and its complications.", "claims": [{"id": "claim-method", "statement": "The DEGs between AMI and sham-operation samples were analyzed using the “Limma” package of R 4.0.3 [12], with |log2FC| > 1.0 and p < 0.05 used as the criteria for statistical significance. Subsequently, these DEGs that were consistently and significantly up-regulated or down-regulated in all 4 groups (i.e., across strains) were identified using the “RobustRankAggreg” package, with |log2FC| > 1.0 and p < 0.05 (corrected for false discovery rate) as the criteria for significance.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36547406", "locator": "sections[4] \"2.2. Screening of Differentially Expressed Genes (DEGs)\" paragraph 2", "quote": "The DEGs between AMI and sham-operation samples were analyzed using the “Limma” package of R 4.0.3 [12], with |log2FC| > 1.0 and p < 0.05 used as the criteria for statistical significance. Subsequently, these DEGs that were consistently and significantly up-regulated or down-regulated in all 4 groups (i.e., across strains) were identified using the “RobustRankAggreg” package, with |log2FC| > 1.0 and p < 0.05 (corrected for false discovery rate) as the criteria for significance."}], "state": "complete"}, {"id": "claim-data-access", "statement": "GSE775: accessed on 2 June 2022, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE775; GSE19322: accessed on 2 June 2022, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19322; GSE110209: accessed on 2 June 2022, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE110209; GSE183168: accessed on 2 June 2022, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE183168; E-MTAB-7376: accessed on 2 June 2022, https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-7376; GSE119857: accessed on 9 November 2022, https://ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE119857.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36547406", "locator": "sections[25] \"notes\" paragraph 1", "quote": "GSE775: accessed on 2 June 2022, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE775; GSE19322: accessed on 2 June 2022, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19322; GSE110209: accessed on 2 June 2022, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE110209; GSE183168: accessed on 2 June 2022, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE183168; E-MTAB-7376: accessed on 2 June 2022, https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-7376; GSE119857: accessed on 9 November 2022, https://ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE119857."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified 10 strongly interlinked hub genes from 135 differentially expressed genes in non-infarcted myocardium after acute myocardial infarction.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36547406", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Ten strongly interlinked hub genes (Timp1, Sparc, Spp1, Tgfb1, Decr1, Vim, Serpine1, Serpina3n, Thbs2, and Vcan) were identified by the construction of a protein–protein interaction network from 135 differentially expressed genes identified through comprehensive bioinformatics analysis and their reliability was verified using GSE119857."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified 10 strongly interlinked hub genes from 135 differentially expressed genes in non-infarcted myocardium after acute myocardial infarction.", "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:36547406"], "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:GSE110209"], "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:GSE110209"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36547406", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/jcdd9120409", "sha256": "sha256:b82356fcacb9ddff24620366f5801319681fcebd2f79d3ce8c4e139616914f18", "bytes": 31507, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/jcdd9120409", "version": null, "note": "Full article fetched from PMC; 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Subsequently, these DEGs that were consistently and significantly up-regulated or down-regulated in all 4 groups (i.e., across strains) were identified using the “RobustRankAggreg” package, with |log2FC| > 1.0 and p < 0.05 (corrected for false discovery rate) as the criteria for significance."}}, {"id": "method-2", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}, {"id": "method-3", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "pathway enrichment"}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE775", "GSE19322", "GSE110209"], "resolved_accessions": ["GSE775", "GSE19322", "GSE110209"], "statements": ["GSE775: accessed on 2 June 2022, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE775; GSE19322: accessed on 2 June 2022, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19322; GSE110209: accessed on 2 June 2022, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE110209; GSE183168: accessed on 2 June 2022, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE183168; E-MTAB-7376: accessed on 2 June 2022, https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-7376; GSE119857: accessed on 9 November 2022, https://ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE119857."], "basis": "The paper names GSE775, GSE19322, GSE110209 in gene expression omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:36547406", "data:geo:GSE110209"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE110209"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:20:38Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 9500, "completion_tokens": 2647, "cached_tokens": 256}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:36547406", "type": "paper", "label": "pmid:36547406"}, {"id": "source:pmid:36547406", "type": "manuscript", "label": "PMID 36547406 full text"}, {"id": "data:geo:GSE110209", "type": "dataset", "label": "GEO GSE110209"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36547406", "type": "paper", "label": "pmid:36547406"}, {"id": "source:pmid:36547406", "type": "manuscript", "label": "PMID 36547406 full text"}, {"id": "data:geo:GSE110209", "type": "dataset", "label": "GEO GSE110209"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36547406", "type": "extraction", "used": ["source:pmid:36547406"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE110209", "type": "accession_resolution", "used": ["data:geo:GSE110209"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:36547406", "parent_hash": "sha256:0482338544c6448f2f435d8e0bb54b045c68405cc19acdbb7f06b64b230672e6", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE110209 licence not read", "asset:data:geo:GSE110209 not downloaded", "asset:data:geo:GSE19322 licence not read", "asset:data:geo:GSE19322 not downloaded", "asset:data:geo:GSE775 licence not read", "asset:data:geo:GSE775 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The DEGs between AMI and sham-operation samples were analyzed using the “Limma” package of R 4.0.3 [12], with |log2FC| > 1.0 and p < 0.05 used as the criteria for statistical significance. Subsequently, these DEGs that were consistently and significantly up-regulated or down-regulated in all 4 groups (i.e., across strains) were identified using the “RobustRankAggreg” package, with |log2FC| > 1.0 and p < 0.05 (corrected for false discovery rate) as the criteria for significance."], "order_basis": "analysis_only", "id": "assay:1"}]}