Identification of Independent and Communal Differentially Expressed Genes as Well as Potential Therapeutic Targets in Ischemic Heart Failure and Non-Ischemic Heart Failure.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34163213", "kind": "science-record", "revision": 9, "content_hash": "sha256:4f8ff937d4dde07b462f4a902185090d7d358e0b9d8a46a89ffb0ac8a6336a00", "created_at": "2026-11-01T15:41:39Z", "updated_at": "2026-11-01T22:46:54Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Independent and Communal Differentially Expressed Genes as Well as Potential Therapeutic Targets in Ischemic Heart Failure and Non-Ischemic Heart Failure.", "doi": "10.2147/PGPM.S313621", "pmid": "34163213", "authors": ["Zuoxiang Wang", "Mingyang Zhang", "Yinan Xu", "Yiyu Gu", "Yumeng Song", "Tingbo Jiang"], "journal": "Pharmacogenomics and personalized medicine", "year": 2021, "abstract": "BACKGROUND: Heart failure (HF) is a rapidly growing public health problem, and its two main etiological types are non-ischemic heart failure (NIHF) and ischemic heart failure (IHF). However, the independent and common mechanisms of NIHF and IHF have not been fully elucidated. Here, bioinformatic analysis was used to characterize the difference and independent pathways for IHF and NIHF, and more importantly, to unearth the common potential markers and therapeutic targets in IHF and NIHF.\nMETHODS: Two data sets with accession numbers GSE26887 and GSE84796 were downloaded from the Gene Expression Omnibus (GEO) database. After identifying the independent and communal DEGs of NIHF and IHF, a functional annotation, protein-protein interaction (PPI) network analysis, co-expression and drug-gene interaction prediction analysis, and mRNA-miRNA regulatory network analysis were performed for DEGs.\nRESULTS: We found 1146 independent DEGs (DEGs2) of NIHF mainly enriched in transcription-related and 2595 independent DEGs (DEGs3) of IHF mainly enriched in immune-related. Moreover, 185 communal DEGs (DEGs1) were found between NIHF and IHF, including 93 upregulated genes and 92 downregulated genes. Pathway enrichment analysis results showed that GPCR pathways and biological processes are closely related to the occurrence of HF. In addition, three hub genes were identified from PPI network, including CCL5, C5 and TLR3.\nCONCLUSION: The identification of DEGs and hub genes in this study contributes to a novel perception for potential functional mechanisms and biomarkers or therapeutic targets in NIHF and IHF.", "claims": [{"id": "claim-method", "statement": "GEO2R is based on limma package that comes with the GEO databases.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34163213", "locator": "sections[4] \"Identification of DEGs\" paragraph 2", "quote": "GEO2R is based on limma package that comes with the GEO databases."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Finally, two datasets were selected from GEO: accession numbers GSE84796 (8 NIHF patients and 10 controls) and GSE26887 (12 IHF patients and 5 controls).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34163213", "locator": "sections[3] \"Data Source\" paragraph 2", "quote": "Finally, two datasets were selected from GEO: accession numbers GSE84796 (8 NIHF patients and 10 controls) and GSE26887 (12 IHF patients and 5 controls)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:34163213"], "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:GSE26887"], "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:GSE26887"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34163213", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/PGPM.S313621", "sha256": "sha256:922ed6f4f27654c6f34620cfc2ec467c995eccd3c5ac2f9fee7d192d544dfcbb", "bytes": 24347, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/PGPM.S313621", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8214211", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE26887", "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=GSE26887", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE26887", "version": null, "note": "Finally, two datasets were selected from GEO: accession numbers GSE84796 (8 NIHF patients and 10 controls) and GSE26887 (12 IHF patients and 5 controls).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Finally, two datasets were selected from GEO: accession numbers GSE84796 (8 NIHF patients and 10 controls) and GSE26887 (12 IHF patients and 5 controls).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM662158", "GSM662159", "GSM662160", "GSM662161", "GSM662162", "GSM662163", "GSM662164", "GSM662165", "GSM662166", "GSM662167", "GSM662168", "GSM662169", "GSM662170", "GSM662171", "GSM662172", "GSM662173", "GSM662174", "GSM662175", "GSM662176", "GSM662177", "GSM662178", "GSM662179", "GSM662180", "GSM662181"], "sample_count": 24, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Transcriptome analysis of diabetic and non diabetic patients affected by post-ischemic heart failure", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": 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"note": "The GO Enrichment Analysis of DEGs2 and DEGs3 (Top 4 Terms According to p.adjust)", "structure": {"pmcid": "PMC8214211", "section_index": 11, "section_title": "GO Enrichment Analyses of Independent DEGs in IHF and NIHF", "row_count": 25, "column_count": 6}, "table": {"label": "Table 1", "caption": "The GO Enrichment Analysis of DEGs2 and DEGs3 (Top 4 Terms According to p.adjust)", "rows": [["DEGs", "Ontology", "ID", "Description", "Counts", "P-value"], ["DEGs2", "BP", "GO:1902895", "Positive regulation of pri-miRNA", "9", "1.00E-05"], ["", "", "GO:0006865", "Transcription from RNA polymerase II promoter amino acid transport", "11", "2.46E-05"], ["", "", "GO:0008360", "Regulation of cell shape", "22", "7.99E-05"], ["", "", "GO:0050900", "Leukocyte migration", "20", "0.000103362"], ["", "CC", "GO:0070062", "Extracellular exosome", "221", "5.37E-07"], ["", "", "GO:0031012", "Extracellular matrix", "38", "7.68E-06"], ["", "", "GO:0005925", "Focal adhesion", "44", "3.64E-05"], ["", "", "GO:0005829", "Cytosol", "237", "1.72E-04"], ["", "MF", "GO:0030169", "Low-density lipoprotein particle binding", "6", "0.001280536"], ["", "", "GO:0015171", "Amino acid transmembrane transporter activity", "10", "0.001473392"], ["", "", "GO:0050786", "RAGE receptor binding", "5", "0.002823533"], ["", "", "GO:0001948", "Glycoprotein binding", "10", "0.013472827"], ["DEGs3", "BP", "GO:0006955", "Immune response", "113", "6.15E-19"], ["", "", "GO:0002250", "Adaptive immune response", "53", "1.50E-14"], ["", "", "GO:0050776", "Regulation of immune response", "55", "4.16E-12"], ["", "", "GO:0045087", "Innate immune response", "93", "7.36E-10"], ["", "CC", "GO:0009897", "External side of plasma membrane", "64", "1.01E-13"], ["", "", "GO:0042101", "T cell receptor complex", "15", "7.68E-11"], ["", "", "GO:0005887", "Integral component of plasma membrane", "221", "4.77E-08"], ["", "", "GO:0005886", "Plasma membrane", "545", "4.96E-07"], ["", "MF", "GO:0004872", "Receptor activity", "56", "2.57E-09"], ["", "", "GO:0004715", "Non-membrane spanning protein", "18", "4.02E-06"], ["", "", "GO:0005515", "Tyrosine kinase activity protein binding", "1057", "3.21E-05"], ["", "", "GO:0005102", "Receptor binding", "64", "8.95E-05"]], "row_count": 25, "column_count": 6, "numeric_cells": 72, "header_rows": 1, "locator": "section[11]/table-wrap[1]#t0001"}}, {"id": "asset:table:pmid:34163213:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:2a7775c807789f77f12d4b90fc0e8163e825af3c0d961586cb9f5314a214ff06", "bytes": 854, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#t0002", "version": null, "note": "The Top 15 Hub Genes Rank in cytoHubba", "structure": {"pmcid": "PMC8214211", "section_index": 13, "section_title": "Hub Gene Selection and Analysis", "row_count": 16, "column_count": 5}, "table": {"label": "Table 2", "caption": "The Top 15 Hub Genes Rank in cytoHubba", "rows": [["BottleNeck", "Closeness", "DMNC", "EPC", "Stress"], ["LRRK2", "LRRK2", "NOC2L", "LRRK2", "LRRK2"], ["PARD3", "TLR3", "P2RY13", "CCL5", "RHOBTB1"], ["BCAR1", "CCL5", "P2RY14", "TLR3", "PARD3"], ["RHOBTB1", "RHOBTB1", "C5", "P2RY14", "BCAR1"], ["RRAD", "TUBB4B", "NOP16", "IFIT2", "NF2"], ["TLR3", "TUBB2A", "RRP12", "C5", "TLR3"], ["NF2", "RRAD", "BYSL", "TUBB4B", "WWC1"], ["CCL5", "CFL2", "PES1", "TUBB2A", "NOP16"], ["WWC1", "IFIT2", "TUBB2A", "P2RY13", "RRAD"], ["NOP16", "BCAR1", "TUBB4B", "CASP1", "CCL5"], ["C5", "DYNC2H1", "TLR3", "RRAD", "PES1"], ["CFL2", "C5", "CCL5", "DYNC2H1", "RPL27A"], ["CD59", "CASP1", "SLC5A6", "SAMD9L", "C5"], ["TUBB4B", "P2RY14", "SLC16A9", "RHOBTB1", "DYNC2H1"], ["BYSL", "CTSK", "XAF1", "CFL2", "CD59"]], "row_count": 16, "column_count": 5, "numeric_cells": 13, "header_rows": 1, "locator": "section[13]/table-wrap[1]#t0002"}}], "gaps": ["asset:data:geo:GSE26887 not downloaded", "asset:data:geo:GSE26887 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