Identification of four hub genes in venous thromboembolism via weighted gene coexpression network analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34861826", "kind": "science-record", "revision": 3, "content_hash": "sha256:6a084ef92a1bd5ad79d180d7725c74c41b36f4708076a0770803700ef0b65b36", "created_at": "2026-11-01T17:36:33Z", "updated_at": "2026-11-01T21:26:43Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of four hub genes in venous thromboembolism via weighted gene coexpression network analysis.", "doi": "10.1186/s12872-021-02409-4", "pmid": "34861826", "authors": ["Guoju Fan", "Zhihai Jin", "Kaiqiang Wang", "Huitang Yang", "Jun Wang", "Yankui Li", "Bo Chen", "Hongwei Zhang"], "journal": "BMC cardiovascular disorders", "year": 2021, "abstract": "BACKGROUND: The pathogenic mechanisms of venous thromboembolism (VT) remain to be defined. This study aimed to identify differentially expressed genes (DEGs) that could serve as potential therapeutic targets for VT.\nMETHODS: Two human datasets (GSE19151 and GSE48000) were analyzed by the robust rank aggregation method. Gene ontology and Kyoto encyclopedia of genes and genomes pathway enrichment analyses were conducted for the DEGs. To explore potential correlations between gene sets and clinical features and to identify hub genes, we utilized weighted gene coexpression network analysis (WGCNA) to build gene coexpression networks incorporating the DEGs. Then, the levels of the hub genes were analyzed in the GSE datasets. Based on the expression of the hub genes, the possible pathways were explored by gene set enrichment analysis and gene set variation analysis. Finally, the diagnostic value of the hub genes was assessed by receiver operating characteristic (ROC) analysis in the GEO database.\nRESULTS: In this study, we identified 54 upregulated and 10 downregulated genes that overlapped between normal and VT samples. After performing WGCNA, the magenta module was the module with the strongest negative correlation with the clinical characteristics. From the key module, FECH, GYPA, RPIA and XK were chosen for further validation. We found that these genes were upregulated in VT samples, and high expression levels were related to recurrent VT. Additionally, the four hub genes might be highly correlated with ribosomal and metabolic pathways. The ROC curves suggested a diagnostic value of the four genes for VT.\nCONCLUSIONS: These results indicated that FECH, GYPA, RPIA and XK could be used as promising biomarkers for the prognosis and prediction of VT.", "claims": [{"id": "claim-method", "statement": "The DEGs that met the criteria of adjusted p value < 0.05 and log 2-fold change (FC) > 0.5 were filtered by robust rank aggregation (RRA) [16].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34861826", "locator": "sections[4] \"Identification of robust DEGs\" paragraph 2", "quote": "The DEGs that met the criteria of adjusted p value < 0.05 and log 2-fold change (FC) > 0.5 were filtered by robust rank aggregation (RRA) [16]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The gene expression profiles of GSE19151 and GSE48000 were downloaded from Gene Expression Omnibus (GEO).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34861826", "locator": "sections[26] \"Availability of data and materials\" paragraph 2", "quote": "The gene expression profiles of GSE19151 and GSE48000 were downloaded from Gene Expression Omnibus (GEO)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified 54 upregulated and 10 downregulated genes that overlapped between normal and VT samples.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34861826", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "In this study, we identified 54 upregulated and 10 downregulated genes that overlapped between normal and VT samples."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified 54 upregulated and 10 downregulated genes that overlapped between normal and VT samples.", "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:34861826"], "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:GSE19151"], "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:GSE19151"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34861826", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12872-021-02409-4", "sha256": "sha256:56f64d762e14df1bba6074386794c6de764362a4a88dfaf9659a0f3d1d9155b7", "bytes": 31175, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12872-021-02409-4", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8642897", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE19151", "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=GSE19151", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE19151", "version": null, "note": "The gene expression profiles of GSE19151 and GSE48000 were downloaded from Gene Expression Omnibus (GEO).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The gene expression profiles of GSE19151 and GSE48000 were downloaded from Gene Expression Omnibus (GEO).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM474708", "GSM474709", "GSM474710", "GSM474711", "GSM474712", "GSM474713", "GSM474714", "GSM474715", "GSM474716", "GSM474717", "GSM474718", "GSM474719", "GSM474720", "GSM474721", "GSM474722", "GSM474723", "GSM474724", "GSM474725", "GSM474726", "GSM474727", "GSM474728", "GSM474729", "GSM474730", "GSM474731", "GSM474732", "GSM474733", "GSM474734", "GSM474735", "GSM474736", "GSM474737", "GSM474738", "GSM474739", "GSM474740", "GSM474741", "GSM474742", "GSM474743", "GSM474744", "GSM474745", "GSM474746", "GSM474747", "GSM474748", "GSM474749", "GSM474750", "GSM474751", "GSM474752", "GSM474753", "GSM474754", "GSM474755", "GSM474756", "GSM474757", "GSM474758", "GSM474759", "GSM474760", "GSM474761", "GSM474762", "GSM474763", "GSM474764", "GSM474765", "GSM474766", "GSM474767", "GSM474768", "GSM474769", "GSM474770", "GSM474771", "GSM474772", "GSM474773", "GSM474774", "GSM474775", "GSM474776", "GSM474777", "GSM474778", "GSM474779", "GSM474780", "GSM474781", "GSM474782", "GSM474783", "GSM474784", "GSM474785", "GSM474786", "GSM474787", "GSM474788", "GSM474789", "GSM474790", "GSM474791", "GSM474792", "GSM474793", "GSM474794", "GSM474795", "GSM474796", "GSM474797", "GSM474798", "GSM474799", "GSM474800", "GSM474801", "GSM474802", "GSM474803", "GSM474804", "GSM474805", "GSM474806", "GSM474807", "GSM474808", "GSM474809", "GSM474810", "GSM474811", "GSM474812", "GSM474813", "GSM474814", "GSM474815", "GSM474816", "GSM474817", "GSM474818", "GSM474819", "GSM474820", "GSM474821", "GSM474822", "GSM474823", "GSM474824", "GSM474825", "GSM474826", "GSM474827", "GSM474828", "GSM474829", "GSM474830", "GSM474831", "GSM474832", "GSM474833", "GSM474834", "GSM474835", "GSM474836", "GSM474837", "GSM474838", "GSM474839", "GSM474840"], "sample_count": 133, "group_sizes": null, "group_sizes_basis": null, "platform": "571", "taxon": "Homo sapiens", "title": "Whole Blood Gene Expression Profiles Distinguish Patients with Single versus Recurrent Venous Thromboembolism", "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:GSE48000", "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=GSE48000", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE48000", "version": null, "note": "The gene expression profiles of GSE19151 and GSE48000 were downloaded from Gene Expression Omnibus (GEO).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The gene expression profiles of GSE19151 and GSE48000 were downloaded from Gene Expression Omnibus (GEO).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1164706", "GSM1164707", "GSM1164708", "GSM1164709", "GSM1164710", "GSM1164711", "GSM1164712", "GSM1164713", "GSM1164714", "GSM1164715", "GSM1164716", "GSM1164717", "GSM1164718", "GSM1164719", "GSM1164720", "GSM1164721", "GSM1164722", "GSM1164723", "GSM1164724", "GSM1164725", "GSM1164726", "GSM1164727", "GSM1164728", "GSM1164729", "GSM1164730", "GSM1164731", "GSM1164732", "GSM1164733", "GSM1164734", "GSM1164735", "GSM1164736", "GSM1164737", "GSM1164738", "GSM1164739", "GSM1164740", "GSM1164741", "GSM1164742", "GSM1164743", "GSM1164744", "GSM1164745", "GSM1164746", "GSM1164747", "GSM1164748", "GSM1164749", "GSM1164750", "GSM1164751", "GSM1164752", "GSM1164753", "GSM1164754", "GSM1164755", "GSM1164756", "GSM1164757", "GSM1164758", "GSM1164759", "GSM1164760", "GSM1164761", "GSM1164762", "GSM1164763", "GSM1164764", "GSM1164765", "GSM1164766", "GSM1164767", "GSM1164768", "GSM1164769", "GSM1164770", "GSM1164771", "GSM1164772", "GSM1164773", "GSM1164774", "GSM1164775", "GSM1164776", "GSM1164777", "GSM1164778", "GSM1164779", "GSM1164780", "GSM1164781", "GSM1164782", "GSM1164783", "GSM1164784", "GSM1164785", "GSM1164786", "GSM1164787", "GSM1164788", "GSM1164789", "GSM1164790", "GSM1164791", "GSM1164792", "GSM1164793", "GSM1164794", "GSM1164795", "GSM1164796", "GSM1164797", "GSM1164798", "GSM1164799", "GSM1164800", "GSM1164801", "GSM1164802", "GSM1164803", "GSM1164804", "GSM1164805", "GSM1164806", "GSM1164807", "GSM1164808", "GSM1164809", "GSM1164810", "GSM1164811", "GSM1164812", "GSM1164813", "GSM1164814", "GSM1164815", "GSM1164816", "GSM1164817", "GSM1164818", "GSM1164819", "GSM1164820", "GSM1164821", "GSM1164822", "GSM1164823", "GSM1164824", "GSM1164825", "GSM1164826", "GSM1164827", "GSM1164828", "GSM1164829", "GSM1164830", "GSM1164831", "GSM1164832", "GSM1164833", "GSM1164834", "GSM1164835", "GSM1164836", "GSM1164837"], "sample_count": 132, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Whole blood gene expression profiles distinguish clinical phenotypes of venous thromboembolism [Set1]", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE19151 not downloaded", "asset:data:geo:GSE19151 licence not read", "asset:data:geo:GSE48000 not downloaded", "asset:data:geo:GSE48000 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": "Robust rank aggregation (RRA)", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The DEGs that met the criteria of adjusted p value < 0.05 and log 2-fold change (FC) > 0.5 were filtered by robust rank aggregation (RRA) [16]."}}], "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": ["GSE19151", "GSE48000"], "resolved_accessions": ["GSE19151", "GSE48000"], "statements": ["The gene expression profiles of GSE19151 and GSE48000 were downloaded from Gene Expression Omnibus (GEO)."], "basis": "The paper names GSE19151, GSE48000 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": ["pathway_enrich"], "assets": ["source:pmid:34861826", "data:geo:GSE19151"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE19151"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:09:37Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 10514, "completion_tokens": 1213, "cached_tokens": 128}}, "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:34861826", "type": "paper", "label": "pmid:34861826"}, {"id": "source:pmid:34861826", "type": "manuscript", "label": "PMID 34861826 full text"}, {"id": "data:geo:GSE19151", "type": "dataset", "label": "GEO GSE19151"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34861826", "type": "paper", "label": "pmid:34861826"}, {"id": "source:pmid:34861826", "type": "manuscript", "label": "PMID 34861826 full text"}, {"id": "data:geo:GSE19151", "type": "dataset", "label": "GEO GSE19151"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34861826", "type": "extraction", "used": ["source:pmid:34861826"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE19151", "type": "accession_resolution", "used": ["data:geo:GSE19151"], "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:34861826", "parent_hash": "sha256:3d916a0c0b1119126894f6fa453e6579a78dbd0bb0b614dd08dd1312a3d6b738", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE19151 licence not read", "asset:data:geo:GSE19151 not downloaded", "asset:data:geo:GSE48000 licence not read", "asset:data:geo:GSE48000 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": "analysis_only", "id": "assay:1"}]}