Bioinformatics and Immune Infiltration Analyses Reveal the Key Pathway and Immune Cells in the Pathogenesis of Hypertrophic Cardiomyopathy.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34497835", "kind": "science-record", "revision": 5, "content_hash": "sha256:7ed315a7b8875a47572c77e71aef654e0d7bacd28e405cae06f2dd52ccc21d3e", "created_at": "2026-11-01T15:41:51Z", "updated_at": "2026-11-01T22:04:40Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics and Immune Infiltration Analyses Reveal the Key Pathway and Immune Cells in the Pathogenesis of Hypertrophic Cardiomyopathy.", "doi": "10.3389/fcvm.2021.696321", "pmid": "34497835", "authors": ["Xu-Zhe Zhang", "Si Zhang", "Ting-Ting Tang", "Xiang Cheng"], "journal": "Frontiers in cardiovascular medicine", "year": 2021, "abstract": "Objective: This study was designed to identify the key pathway and immune cells for hypertrophic cardiomyopathy (HCM) via bioinformatics analyses of public datasets and evaluate the significance of immune infiltration in the pathogenesis of HCM. Methods: Expressional profiling from two public datasets (GSE36961 and GSE141910) of human HCM and healthy control cardiac tissues was obtained from the GEO database. After data preprocessing, differentially expressed genes (DEGs) were then screened between HCM and healthy control cardiac tissues in parallel. Gene Ontology, pathway functional enrichment, and gene set enrichment analysis were performed using DAVID and GSEA application. The compositional patterns of immune and stromal cells in HCM and control cardiac tissues were estimated based on the merged data using xCell. Protein-protein interaction (PPI) network and module analyses were constructed by STRING and Cytoscape applications. Gender-based expressional differences analyses were also conducted to explore gender differences in HCM. GSE130036 and clinical samples were used for verification analyses. Results: A total of 310 DEGs were identified. Upregulated DEGs were mainly enriched in \"adhesion\" and \"apoptotic process\" in the biological process. As for the downregulated DEGs, \"inflammatory response,\" \"innate immune response,\" \"phagosome,\" and \"JAK-STAT signaling pathway\" were highly enriched. Immune infiltration analyses suggested that the scores of macrophages, monocytes, DC, Th1, Treg, and plasma cells in the HCM group were significantly decreased, while CD8+ T cells, basophils, fibroblasts, and platelets were significantly enriched. Module analyses revealed that STAT3, as the hub genes in HCM together with LYVE1+CD163+ macrophages, may play a key role in the pathogenesis of HCM while there were no obvious gender differences in the HCM samples from selected datasets. Verification analyses performed on GSE130036 and clinical samples showed a strong positive correlation (Spearman correlation = 0.7646) and a good co-localization relationship between LYVE1 and CD163, suggesting the potential function of LYVE1+CD163+ macrophages in maintaining the homeostasis of cardiac tissue. Conclusion: STAT3-related pathway and CD163+LYVE1+ macrophages were identified as the potential key pathway and immune cells in HCM and may serve as interesting targets for further in-depth research.", "claims": [{"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. 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"missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: spearman."}, "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": ["GSE36961", "GSE141910", "GSE130036"], "resolved_accessions": ["GSE36961", "GSE141910", "GSE130036"], "statements": ["The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material."], "basis": "The paper names GSE36961, GSE141910, GSE130036 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": ["spearman_rho"], "assets": ["source:pmid:34497835", "data:geo:GSE130036", "asset:table:pmid:34497835:1", "asset:table:pmid:34497835:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE130036"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T19:47:56Z", "independence": "single_reader"}, "evidence_check": {"method": null, "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 33211, "completion_tokens": 1638, "cached_tokens": 776}}, "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:34497835", "type": "paper", "label": "pmid:34497835"}, {"id": "source:pmid:34497835", "type": "manuscript", "label": "PMID 34497835 full text"}, {"id": "data:geo:GSE130036", "type": "dataset", "label": "GEO GSE130036"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34497835", "type": "paper", "label": "pmid:34497835"}, {"id": "source:pmid:34497835", "type": "manuscript", "label": "PMID 34497835 full text"}, {"id": "data:geo:GSE130036", "type": "dataset", "label": "GEO GSE130036"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34497835", "type": "extraction", "used": ["source:pmid:34497835"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE130036", "type": "accession_resolution", "used": ["data:geo:GSE130036"], "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:34497835", "parent_hash": "sha256:ec9d3af51240b6d5887d6869cf5a4c66f08c16ff5f821048528cbaf978aee390", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE130036 licence not read", "asset:data:geo:GSE130036 not downloaded", "asset:data:geo:GSE141910 licence not read", "asset:data:geo:GSE141910 not downloaded", "asset:data:geo:GSE36961 licence not read", "asset:data:geo:GSE36961 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "correlation_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["spearman_rho"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["Spearman correlation"], "order_basis": "analysis_only", "id": "assay:1"}]}