Identification and analysis of key genes associated with acute myocardial infarction by integrated bioinformatics methods.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33847684", "kind": "science-record", "revision": 8, "content_hash": "sha256:f1f0e1dbe37d58a800fc746b9d20ca28afcb2f1712c733f1f173a564f7b2f5a7", "created_at": "2026-11-01T15:41:32Z", "updated_at": "2026-11-01T22:46:30Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and analysis of key genes associated with acute myocardial infarction by integrated bioinformatics methods.", "doi": "10.1097/MD.0000000000025553", "pmid": "33847684", "authors": ["Siyu Guo", "Jiarui Wu", "Wei Zhou", "Xinkui Liu", "Yingying Liu", "Jingyuan Zhang", "Shanshan Jia", "Jialin Li", "Haojia Wang"], "journal": "Medicine", "year": 2021, "abstract": "BACKGROUND: Acute myocardial infarction (AMI) is a common disease leading threat to human health around the world. Here we aimed to explore new biomarkers and potential therapeutic targets in AMI through adopting integrated bioinformatics tools.\nMETHODS: The gene expression Omnibus (GEO) database was used to obtain genes data of AMI and no-AMI whole blood. Furthermore, differentially expressed genes (DEGs) were screened using the \"Limma\" package in R 3.6.1 software. Functional and pathway enrichment analyses of DEGs were performed via \"Bioconductor\" and \"GOplot\" package in R 3.6.1 software. In order to screen hub DEGs, the STRING version 11.0 database, Cytoscape and molecular complex detection (MCODE) were applied. Correlation among the hub DEGs was evaluated using Pearson's correlation analysis.\nRESULTS: By performing DEGs analysis, 289 upregulated and 62 downregulated DEGs were successfully identified from GSE66360, respectively. And they were mainly enriched in the terms of neutrophil activation, immune response, cytokine, nuclear factor kappa-B (NF-κB) signaling pathway, IL-17 signaling pathway, and tumor necrosis factor (TNF) signaling pathway. Based on the data of protein-protein interaction (PPI), the top 10 hub genes were ranked, including interleukin-8 (CXCL8), TNF, N-formyl peptide receptor 2 (FPR2), growth-regulated alpha protein (CXCL1), transcription factor AP-1 (JUN), interleukin-1 beta (IL1B), platelet basic protein (PPBP), matrix metalloproteinase-9 (MMP9), toll-like receptor 2 (TLR2), and high affinity immunoglobulin epsilon receptor subunit gamma (FCER1G). What's more, the results of correlation analysis demonstrated that there was positive correlation between the 10 hub DEGs.\nCONCLUSION: Ten DEGs were identified as potential candidate diagnostic biomarkers for patients with AMI in present study. However, further experiments are needed to confirm the functional pathways and hub genes associated with AMI.", "claims": [{"id": "claim-method", "statement": "Using the “Limma” package in R 3.6.1 software,[20] normalization, log 2 conversion and DEGs screening of GSE66360 matrix data were performed. |log2FC| > 1 and adjust P-value < .05 were regarded as the statistical significance threshold level of DEGs samples.[21,22]", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33847684", "locator": "sections[4] \"Screening of DEGs and correlation analysis\" paragraph 2", "quote": "Using the “Limma” package in R 3.6.1 software,[20] normalization, log 2 conversion and DEGs screening of GSE66360 matrix data were performed. |log2FC| > 1 and adjust P-value < .05 were regarded as the statistical significance threshold level of DEGs samples.[21,22]"}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33847684", "locator": "sections[18] \"fn-group\" paragraph 1", "quote": "The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:33847684"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "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": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33847684", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1097/MD.0000000000025553", "sha256": "sha256:1d5f8c194cca58b6d4ac515fda4d5777a43f068c847e62cfa9d7707bb7cf779b", "bytes": 24725, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1097/MD.0000000000025553", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8052032", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:33847684:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e10769fb4e72096e9fea25c9eb956da9ee5eaa12e7f375fcaddac6fc3a80c1ec", "bytes": 886, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#T1", "version": null, "note": "The information of top 10 hub genes based on their degree value.", "structure": {"pmcid": "PMC8052032", "section_index": 6, "section_title": "PPI network construction and module analysis", "row_count": 11, "column_count": 5}, "table": {"label": "Table 1", "caption": "The information of top 10 hub genes based on their degree value.", "rows": [["Gene name", "Protein name", "Expression level", "Degree", "Enriched significant modules"], ["CXCL8", "Interleukin-8", "Up", "38", "Module 1"], ["TNF", "Tumor necrosis factor", "Up", "35", "None"], ["FPR2", "N-formyl peptide receptor 2", "Up", "35", "Module 1"], ["CXCL1", "Growth-regulated alpha protein", "Up", "33", "Module 1"], ["JUN", "Transcription factor AP-1", "Up", "31", "Module 2"], ["IL1B", "Interleukin-1 beta", "Up", "30", "Module 2"], ["PPBP", "Platelet basic protein", "Up", "29", "Module 1"], ["MMP9", "Matrix metalloproteinase-9", "Up", "26", "Module 1"], ["TLR2", "Toll-like receptor 2", "Up", "25", "None"], ["FCER1G", "High affinity immunoglobulin epsilon receptor subunit gamma", "Up", "25", "Module 1"]], "row_count": 11, "column_count": 5, "numeric_cells": 24, "header_rows": 1, "locator": "section[12]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:33847684:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e10769fb4e72096e9fea25c9eb956da9ee5eaa12e7f375fcaddac6fc3a80c1ec", "bytes": 886, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#T1", "version": null, "note": "The information of top 10 hub genes based on their degree value.", "structure": {"pmcid": "PMC8052032", "section_index": 12, "section_title": "PPI network construction and module analysis", "row_count": 11, "column_count": 5}, "table": {"label": "Table 1", "caption": "The information of top 10 hub genes based on their degree value.", "rows": [["Gene name", "Protein name", "Expression level", "Degree", "Enriched significant modules"], ["CXCL8", "Interleukin-8", "Up", "38", "Module 1"], ["TNF", "Tumor necrosis factor", "Up", "35", "None"], ["FPR2", "N-formyl peptide receptor 2", "Up", "35", "Module 1"], ["CXCL1", "Growth-regulated alpha protein", "Up", "33", "Module 1"], ["JUN", "Transcription factor AP-1", "Up", "31", "Module 2"], ["IL1B", "Interleukin-1 beta", "Up", "30", "Module 2"], ["PPBP", "Platelet basic protein", "Up", "29", "Module 1"], ["MMP9", "Matrix metalloproteinase-9", "Up", "26", "Module 1"], ["TLR2", "Toll-like receptor 2", "Up", "25", "None"], ["FCER1G", "High affinity immunoglobulin epsilon receptor subunit gamma", "Up", "25", "Module 1"]], "row_count": 11, "column_count": 5, "numeric_cells": 24, "header_rows": 1, "locator": "section[12]/table-wrap[1]#T1"}}], "gaps": []}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Using the “Limma” package in R 3.6.1 software,[20] normalization, log 2 conversion and DEGs screening of GSE66360 matrix data were performed. |log2FC| > 1 and adjust P-value < .05 were regarded as the statistical significance threshold level of DEGs samples.[21,22]"}}, {"id": "method-2", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.7, "band": "medium", "quote": "Pearson's correlation"}}, {"id": "method-3", "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-4", "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": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "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": "R4", "reachable": false, "accessions": [], "resolved_accessions": [], "statements": ["The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request."], "basis": "The paper names no accession to its source data, so the data has to come from the authors."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:33847684", "asset:table:pmid:33847684:1", "asset:table:pmid:33847684:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T19:31:04Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 19458, "completion_tokens": 1063, "cached_tokens": 784}}, "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:33847684", "type": "paper", "label": "pmid:33847684"}, {"id": "source:pmid:33847684", "type": "manuscript", "label": "PMID 33847684 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33847684", "type": "paper", "label": "pmid:33847684"}, {"id": "source:pmid:33847684", "type": "manuscript", "label": "PMID 33847684 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33847684", "type": "extraction", "used": ["source:pmid:33847684"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "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:33847684", "parent_hash": "sha256:2b9303e8a4caf2ed757662709724b1bd70d20d30637ccfdd25c54648f1b3a0bf", "fork_of": null, "generation": 7}, "gaps": ["execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"], "assays": [{"role": "data_generation", "definition_id": "clinical_cohort", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.85, "evidence": ["otential candidate diagnostic biomarkers for patients with AMI in present study. However, further exper"], "order_basis": "paper_text_order:1888", "id": "assay:1"}, {"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": ["Using the “Limma” package in R 3.6.1 software,[20] normalization, log 2 conversion and DEGs screening of GSE66360 matrix data were performed. |log2FC| > 1 and adjust P-value < .05 were regarded as the statistical significance threshold level of DEGs samples.[21,22]"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}