Identifying key genes associated with acute myocardial infarction.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29049183", "kind": "science-record", "revision": 7, "content_hash": "sha256:514640993795507ad0a1a64c6ae04baa9c7fbc5a8a2052182d93528d4d07e32f", "created_at": "2026-11-01T15:40:29Z", "updated_at": "2026-11-01T21:21:07Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identifying key genes associated with acute myocardial infarction.", "doi": "10.1097/MD.0000000000007741", "pmid": "29049183", "authors": ["Ming Cheng", "Shoukuan An", "Junquan Li"], "journal": "Medicine", "year": 2017, "abstract": "BACKGROUND: This study aimed to identify key genes associated with acute myocardial infarction (AMI) by reanalyzing microarray data.\nMETHODS: Three gene expression profile datasets GSE66360, GSE34198, and GSE48060 were downloaded from GEO database. After data preprocessing, genes without heterogeneity across different platforms were subjected to differential expression analysis between the AMI group and the control group using metaDE package. P < .05 was used as the cutoff for a differentially expressed gene (DEG). The expression data matrices of DEGs were imported in ReactomeFIViz to construct a gene functional interaction (FI) network. Then, DEGs in each module were subjected to pathway enrichment analysis using DAVID. MiRNAs and transcription factors predicted to regulate target DEGs were identified. Quantitative real-time polymerase chain reaction (RT-PCR) was applied to verify the expression of genes.\nRESULT: A total of 913 upregulated genes and 1060 downregulated genes were identified in the AMI group. A FI network consists of 21 modules and DEGs in 12 modules were significantly enriched in pathways. The transcription factor-miRNA-gene network contains 2 transcription factors FOXO3 and MYBL2, and 2 miRNAs hsa-miR-21-5p and hsa-miR-30c-5p. RT-PCR validations showed that expression levels of FOXO3 and MYBL2 were significantly increased in AMI, and expression levels of hsa-miR-21-5p and hsa-miR-30c-5p were obviously decreased in AMI.\nCONCLUSION: A total of 41 DEGs, such as SOCS3, VAPA, and COL5A2, are speculated to have roles in the pathogenesis of AMI; 2 transcription factors FOXO3 and MYBL2, and 2 miRNAs hsa-miR-21-5p and hsa-miR-30c-5p may be involved in the regulation of the expression of these DEGs.", "claims": [{"id": "claim-method", "statement": "Next, genes without heterogeneity were subjected to differential expression analysis of their expression levels between the AMI group and the control group using metaDE package; P < .05 was used as the cutoff for a differentially expressed gene (DEG).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29049183", "locator": "sections[5] \"Heterogeneity test and screening of characteristic genes\" paragraph 2", "quote": "Next, genes without heterogeneity were subjected to differential expression analysis of their expression levels between the AMI group and the control group using metaDE package; P < .05 was used as the cutoff for a differentially expressed gene (DEG)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Three gene expression profile datasets GSE66360, GSE34198, and GSE48060 were downloaded from GEO (Gene Expression Omnibus, http://www.ncbi.nlm.nih.gov/geo/) database. The samples included in each dataset and annotation platform are listed in Table 1.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29049183", "locator": "sections[3] \"Source of microarray data\" paragraph 2", "quote": "Three gene expression profile datasets GSE66360, GSE34198, and GSE48060 were downloaded from GEO (Gene Expression Omnibus, http://www.ncbi.nlm.nih.gov/geo/) database. The samples included in each dataset and annotation platform are listed in Table 1."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using the metaDE package for differential-expression analysis across three GEO microarray datasets, the study identified 913 upregulated and 1060 downregulated genes in the AMI group.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:29049183", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Three gene expression profile datasets GSE66360, GSE34198, and GSE48060 were downloaded from GEO database."}, {"asset": "source:pmid:29049183", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "After data preprocessing, genes without heterogeneity across different platforms were subjected to differential expression analysis between the AMI group and the control group using metaDE package."}, {"asset": "source:pmid:29049183", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 913 upregulated genes and 1060 downregulated genes were identified in the AMI group."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using the metaDE package for differential-expression analysis across three GEO microarray datasets, the study identified 913 upregulated and 1060 downregulated genes in the AMI group.", "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:29049183"], "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:GSE34198"], "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:GSE34198"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:29049183", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1097/MD.0000000000007741", "sha256": "sha256:ea18995c1f6410249d145f2d76e82b4d6ce9e4437ca7e186a0988a95de703b34", "bytes": 27660, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1097/MD.0000000000007741", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5662349", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE34198", "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=GSE34198", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE34198", "version": null, "note": "Three gene expression profile datasets GSE66360, GSE34198, and GSE48060 were downloaded from GEO (Gene Expression Omnibus, http://www.ncbi.nlm.nih.gov/geo/) database. The samples included in each dataset and annotation platform are listed in Table 1.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Three gene expression profile datasets GSE66360, GSE34198, and GSE48060 were downloaded from GEO (Gene Expression Omnibus, http://www.ncbi.nlm.nih.gov/geo/) database. The samples included in each dataset and annotation platform are listed in Table 1.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM843870", "GSM843871", "GSM843872", "GSM843873", "GSM843874", "GSM843875", "GSM843876", "GSM843877", "GSM843878", "GSM843879", "GSM843880", "GSM843881", "GSM843882", "GSM843883", "GSM843884", "GSM843885", "GSM843886", "GSM843887", "GSM843888", "GSM843889", "GSM843890", "GSM843891", "GSM843892", "GSM843893", "GSM843894", "GSM843895", "GSM843896", "GSM843897", "GSM843898", "GSM843899", "GSM843900", "GSM843901", "GSM843902", "GSM843903", "GSM843904", "GSM843905", "GSM843906", "GSM843907", "GSM843908", "GSM843909", "GSM843910", "GSM843911", "GSM843912", "GSM843913", "GSM843914", "GSM843915", "GSM843916", "GSM843917", "GSM843918", "GSM843919", "GSM843920", "GSM843921", "GSM843922", "GSM843923", "GSM843924", "GSM843925", "GSM843926", "GSM843927", "GSM843928", "GSM843929", "GSM843930", "GSM843931", "GSM843932", "GSM843933", "GSM843934", "GSM843935", "GSM843936", "GSM843937", "GSM843938", "GSM843939", "GSM843940", "GSM843941", "GSM843942", "GSM843943", "GSM843944", "GSM843945", "GSM843946", "GSM843947", "GSM843948", "GSM843949", "GSM843950", "GSM843951", "GSM843952", "GSM843953", "GSM843954", "GSM843955", "GSM843956", "GSM843957", "GSM843958", "GSM843959", "GSM843960", "GSM843961", "GSM843962", "GSM843963", "GSM843964", "GSM843965", "GSM843966"], "sample_count": 97, "group_sizes": null, "group_sizes_basis": null, "platform": "6102", "taxon": "Homo sapiens", "title": "Determinants of excess genetic risk of acute myocardial infarction – a matched case-control study", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE48060", "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=GSE48060", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE48060", "version": null, "note": "Three gene expression profile datasets GSE66360, GSE34198, and GSE48060 were downloaded from GEO (Gene Expression Omnibus, http://www.ncbi.nlm.nih.gov/geo/) database. The samples included in each dataset and annotation platform are listed in Table 1.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Three gene expression profile datasets GSE66360, GSE34198, and GSE48060 were downloaded from GEO (Gene Expression Omnibus, http://www.ncbi.nlm.nih.gov/geo/) database. The samples included in each dataset and annotation platform are listed in Table 1.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1167072", "GSM1167073", "GSM1167074", "GSM1167075", "GSM1167076", "GSM1167077", "GSM1167078", "GSM1167079", "GSM1167080", "GSM1167081", "GSM1167082", "GSM1167083", "GSM1167084", "GSM1167085", "GSM1167086", "GSM1167087", "GSM1167088", "GSM1167089", "GSM1167090", "GSM1167091", "GSM1167092", "GSM1167093", "GSM1167094", "GSM1167095", "GSM1167096", "GSM1167097", "GSM1167098", "GSM1167099", "GSM1167100", "GSM1167101", "GSM1167102", "GSM1167103", "GSM1167104", "GSM1167105", "GSM1167106", "GSM1167107", "GSM1167108", "GSM1167109", "GSM1167110", "GSM1167111", "GSM1167112", "GSM1167113", "GSM1167114", "GSM1167115", "GSM1167116", "GSM1167117", "GSM1167118", "GSM1167119", "GSM1167120", "GSM1167121", "GSM1167122", "GSM1167123"], "sample_count": 52, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Transcriptome from circulating cells suggests dysregulated pathways associated with long-term recurrent events following first-time myocardial infarction.", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE66360", "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=GSE66360", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE66360", "version": null, "note": "Three gene expression profile datasets GSE66360, GSE34198, and GSE48060 were downloaded from GEO (Gene Expression Omnibus, http://www.ncbi.nlm.nih.gov/geo/) database. The samples included in each dataset and annotation platform are listed in Table 1.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Three gene expression profile datasets GSE66360, GSE34198, and GSE48060 were downloaded from GEO (Gene Expression Omnibus, http://www.ncbi.nlm.nih.gov/geo/) database. The samples included in each dataset and annotation platform are listed in Table 1.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1620819", "GSM1620820", "GSM1620821", "GSM1620822", "GSM1620823", "GSM1620824", "GSM1620825", "GSM1620826", "GSM1620827", "GSM1620828", "GSM1620829", "GSM1620830", "GSM1620831", "GSM1620832", "GSM1620833", "GSM1620834", "GSM1620835", "GSM1620836", "GSM1620837", "GSM1620838", "GSM1620839", "GSM1620840", "GSM1620841", "GSM1620842", "GSM1620843", "GSM1620844", "GSM1620845", "GSM1620846", "GSM1620847", "GSM1620848", "GSM1620849", "GSM1620850", "GSM1620851", "GSM1620852", "GSM1620853", "GSM1620854", "GSM1620855", "GSM1620856", "GSM1620857", "GSM1620858", "GSM1620859", "GSM1620860", "GSM1620861", "GSM1620862", "GSM1620863", "GSM1620864", "GSM1620865", "GSM1620866", "GSM1620867", "GSM1620868", "GSM1620869", "GSM1620870", "GSM1620871", "GSM1620872", "GSM1620873", "GSM1620874", "GSM1620875", "GSM1620876", "GSM1620877", "GSM1620878", "GSM1620879", "GSM1620880", "GSM1620881", "GSM1620882", "GSM1620883", "GSM1620884", "GSM1620885", "GSM1620886", "GSM1620887", "GSM1620888", "GSM1620889", "GSM1620890", "GSM1620891", "GSM1620892", "GSM1620893", "GSM1620894", "GSM1620895", "GSM1620896", "GSM1620897", "GSM1620898", "GSM1620899", "GSM1620900", "GSM1620901", "GSM1620902", "GSM1620903", "GSM1620904", "GSM1620905", "GSM1620906", "GSM1620907", "GSM1620908", "GSM1620909", "GSM1620910", "GSM1620911", "GSM1620912", "GSM1620913", "GSM1620914", "GSM1620915", "GSM1620916", "GSM1620917"], "sample_count": 99, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "A Whole Blood Molecular Signature for the Identification of Acute Myocardial Infarction Without Relying Upon Myonecrosis (microarray)", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:29049183:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:09f1d70d2b80b283d7bcc883f3b1dcf39882cb01bdd812a56cc27b6b1f5407d0", "bytes": 230, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#T1", "version": null, "note": "Information on platform and study subjects in each gene expression profile dataset.", "structure": {"pmcid": "PMC5662349", "section_index": 3, "section_title": "Source of microarray data", "row_count": 0, "column_count": 0}, "table": {"label": "Table 1", "caption": "Information on platform and study subjects in each gene expression profile dataset.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[3]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:29049183:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3f5891531ea2acffb1d59c8ab5c14d65d28e08f6a999b7d0ee0d1b504e2922ca", "bytes": 206, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#T2", "version": null, "note": "Primers of genes determined by quantitative real-time PCR.", "structure": {"pmcid": "PMC5662349", "section_index": 10, "section_title": "Validation of DEGs", "row_count": 0, "column_count": 0}, "table": {"label": "Table 2", "caption": "Primers of genes determined by quantitative real-time PCR.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[10]/table-wrap[1]#T2"}}, {"id": "asset:table:pmid:29049183:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:dd26b702b6e42d2e88842df3c009f7aacda421897711fafab8ac3c5d4e782d13", "bytes": 268, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#T3", "version": null, "note": "Pathway enrichment analysis of differentially expressed genes in the modules of the gene functional interaction network.", "structure": {"pmcid": "PMC5662349", "section_index": 13, "section_title": "Construction of FI network and pathway enrichment analysis", "row_count": 0, "column_count": 0}, "table": {"label": "Table 3", "caption": "Pathway enrichment analysis of differentially expressed genes in the modules of the gene functional interaction network.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[13]/table-wrap[1]#T3"}}, {"id": "asset:table:pmid:29049183:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:2039d4c086419f1c604d2064d5dba8ce13d74966a96a54c5b25dc617213fddaa", "bytes": 280, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[2]#T4", "version": null, "note": "Pathway enrichment analysis of differentially expressed genes in the modules of the gene functional interaction network.", "structure": {"pmcid": "PMC5662349", "section_index": 13, "section_title": "Construction of FI network and pathway enrichment analysis", "row_count": 0, "column_count": 0}, "table": {"label": "Table 3 (Continued)", "caption": "Pathway enrichment analysis of differentially expressed genes in the modules of the gene functional interaction network.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[13]/table-wrap[2]#T4"}}], "gaps": ["asset:data:geo:GSE34198 not downloaded", "asset:data:geo:GSE34198 licence not read", "asset:data:geo:GSE48060 not downloaded", "asset:data:geo:GSE48060 licence not read", "asset:data:geo:GSE66360 not downloaded", "asset:data:geo:GSE66360 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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"}}, {"id": "method-2", "family": null, "specific": null, "label": "MetaDE differential expression analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Next, genes without heterogeneity were subjected to differential expression analysis of their expression levels between the AMI group and the control group using metaDE package; P < .05 was used as the cutoff for a differentially expressed gene (DEG)."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": ["pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pathway_enrichment."}, "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": ["GSE66360", "GSE34198", "GSE48060"], "resolved_accessions": ["GSE66360", "GSE34198", "GSE48060"], "statements": ["Three gene expression profile datasets GSE66360, GSE34198, and GSE48060 were downloaded from GEO (Gene Expression Omnibus, http://www.ncbi.nlm.nih.gov/geo/) database. The samples included in each dataset and annotation platform are listed in Table 1."], "basis": "The paper names GSE66360, GSE34198, GSE48060 in GEO (Gene Expression Omnibus) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["pathway_enrich"], "assets": ["source:pmid:29049183", "data:geo:GSE34198", "asset:table:pmid:29049183:1", "asset:table:pmid:29049183:2", "asset:table:pmid:29049183:3", "asset:table:pmid:29049183:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE34198"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:32:30Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 8, "usage": {"prompt_tokens": 59575, "completion_tokens": 3674, "cached_tokens": 2088}}, "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:29049183", "type": "paper", "label": "pmid:29049183"}, {"id": "source:pmid:29049183", "type": "manuscript", "label": "PMID 29049183 full text"}, {"id": "data:geo:GSE34198", "type": "dataset", "label": "GEO GSE34198"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:29049183", "type": "paper", "label": "pmid:29049183"}, {"id": "source:pmid:29049183", "type": "manuscript", "label": "PMID 29049183 full text"}, {"id": "data:geo:GSE34198", "type": "dataset", "label": "GEO GSE34198"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-29049183", "type": "extraction", "used": ["source:pmid:29049183"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE34198", "type": "accession_resolution", "used": ["data:geo:GSE34198"], "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:29049183", "parent_hash": "sha256:a2473f2022090259ec0c64eb6eb70c8626cc6083d60f3d2ad7a75ccc19872572", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE34198 licence not read", "asset:data:geo:GSE34198 not downloaded", "asset:data:geo:GSE48060 licence not read", "asset:data:geo:GSE48060 not downloaded", "asset:data:geo:GSE66360 licence not read", "asset:data:geo:GSE66360 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["e myocardial infarction (AMI) by reanalyzing microarray data. METHODS: Three gene expression profile"], "order_basis": "paper_text_order:138", "id": "assay:1"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["hsa-miR-30c-5p determined using quantitative real-time PCR."], "order_basis": "paper_text_order:2764", "id": "assay:2"}, {"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["pathway enrichment"], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}