Analysis of the potential relationship between COVID-19 and Behcet's disease using transcriptome data.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37335738", "kind": "science-record", "revision": 3, "content_hash": "sha256:6f2c8b3d87123e27a753e2b91ad89d34dd3064a35e022b497dacf33829fc76d3", "created_at": "2026-11-01T19:02:04Z", "updated_at": "2026-11-01T22:09:43Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Analysis of the potential relationship between COVID-19 and Behcet's disease using transcriptome data.", "doi": "10.1097/MD.0000000000033821", "pmid": "37335738", "authors": ["Zhibai Zhao", "Chenyu Zhou", "Mengna Zhang", "Ling Qian", "Wenhui Xia", "Yuan Fan"], "journal": "Medicine", "year": 2023, "abstract": "To investigate the potential role of COVID-19 in relation to Behcet's disease (BD) and to search for relevant biomarkers. We used a bioinformatics approach to download transcriptomic data from peripheral blood mononuclear cells (PBMCs) of COVID-19 patients and PBMCs of BD patients, screened the common differential genes between COVID-19 and BD, performed gene ontology (GO) and pathway analysis, and constructed the protein-protein interaction (PPI) network, screened the hub genes and performed co-expression analysis. In addition, we constructed the genes-transcription factors (TFs)-miRNAs network, the genes-diseases network and the genes-drugs network to gain insight into the interactions between the 2 diseases. We used the RNA-seq dataset from the GEO database (GSE152418, GSE198533). We used cross-analysis to obtain 461 up-regulated common differential genes and 509 down-regulated common differential genes, mapped the PPI network, and used Cytohubba to identify the 15 most strongly associated genes as hub genes (ACTB, BRCA1, RHOA, CCNB1, ASPM, CCNA2, TOP2A, PCNA, AURKA, KIF20A, MAD2L1, MCM4, BUB1, RFC4, and CENPE). We screened for statistically significant hub genes and found that ACTB was in low expression of both BD and COVID-19, and ASPM, CCNA2, CCNB1, and CENPE were in low expression of BD and high expression of COVID-19. GO analysis and pathway analysis was then performed to obtain common pathways and biological response processes, which suggested a common association between BD and COVID-19. The genes-TFs-miRNAs network, genes-diseases network and genes-drugs network also play important roles in the interaction between the 2 diseases. Interaction between COVID-19 and BD exists. ACTB, ASPM, CCNA2, CCNB1, and CENPE as potential biomarkers for 2 diseases.", "claims": [{"id": "claim-method", "statement": "The t test was used to compare the 2 data sets and was considered to be significantly different when the P value was less than .05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37335738", "locator": "sections[9] \"2.7. Validation of hub genes expression in the COVID-19 and BD dataset\" paragraph 2", "quote": "The t test was used to compare the 2 data sets and was considered to be significantly different when the P value was less than .05."}], "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:37335738", "locator": "sections[29] \"(untitled)\" 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"}, {"id": "claim-target-result", "statement": "Interaction between COVID-19 and BD exists.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37335738", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Interaction between COVID-19 and BD exists."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Interaction between COVID-19 and BD exists.", "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:37335738"], "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:GSE152418"], "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:GSE152418"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37335738", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1097/MD.0000000000033821", "sha256": "sha256:0347e3c86943b78e8c72633ec11e0a939098475fc1eac3e65096cb938c7f0f5e", "bytes": 54577, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1097/MD.0000000000033821", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10193850", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE152418", "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=GSE152418", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE152418", "version": null, "note": "The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4614985", "GSM4614986", "GSM4614987", "GSM4614988", "GSM4614989", "GSM4614990", "GSM4614991", "GSM4614992", "GSM4614993", "GSM4614994", "GSM4614995", "GSM4614996", "GSM4614997", "GSM4614998", "GSM4614999", "GSM4615000", "GSM4615001", "GSM4615003", "GSM4615006", "GSM4615008", "GSM4615011", "GSM4615014", "GSM4615016", "GSM4615019", "GSM4615022", "GSM4615025", "GSM4615027", "GSM4615030", "GSM4615032", "GSM4615033", "GSM4615034", "GSM4615035", "GSM4615036", "GSM4615037"], "sample_count": 34, "group_sizes": null, "group_sizes_basis": null, "platform": "24676", "taxon": "Homo sapiens", "title": "Systems biological assessment of immunity to severe and mild COVID-19 infections", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE164805", "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=GSE164805", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE164805", "version": null, "note": "The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM5019817", "GSM5019818", "GSM5019819", "GSM5019820", "GSM5019821", "GSM5019822", "GSM5019823", "GSM5019824", "GSM5019825", "GSM5019826", "GSM5019827", "GSM5019828", "GSM5019829", "GSM5019830", "GSM5019831"], "sample_count": 15, "group_sizes": null, "group_sizes_basis": null, "platform": "26963", "taxon": "Homo sapiens", "title": "The transcriptional profiles of severe COVID-19", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE198533", "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=GSE198533", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE198533", "version": null, "note": "The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM5951802", "GSM5951803", "GSM5951804", "GSM5951805", "GSM5951806", "GSM5951807", "GSM5951808", "GSM5951809", "GSM5951810", "GSM5951811", "GSM5951812", "GSM5951813", "GSM5951814", "GSM5951815", "GSM5951816", "GSM5951817", "GSM5951818", "GSM5951819", "GSM5951820"], "sample_count": 19, "group_sizes": null, "group_sizes_basis": null, "platform": "24676", "taxon": "Homo sapiens", "title": "mRNA expression profiling of PBMCs from Behcet’s disease", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE152418 not downloaded", "asset:data:geo:GSE152418 licence not read", "asset:data:geo:GSE164805 not downloaded", "asset:data:geo:GSE164805 licence not read", "asset:data:geo:GSE198533 not downloaded", "asset:data:geo:GSE198533 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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-2", "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": 0.8, "band": "high", "quote": "pathway enrichment"}}, {"id": "method-3", "family": null, "specific": null, "label": "t test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The t test was used to compare the 2 data sets and was considered to be significantly different when the P value was less than .05."}}], "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": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "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": ["GSE152418", "GSE198533", "GSE164805"], "resolved_accessions": ["GSE152418", "GSE198533", "GSE164805"], "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 GSE152418, GSE198533, GSE164805 in GEO database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:37335738", "data:geo:GSE152418"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE152418"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:44:21Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 15178, "completion_tokens": 1626, "cached_tokens": 256}}, "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:37335738", "type": "paper", "label": "pmid:37335738"}, {"id": "source:pmid:37335738", "type": "manuscript", "label": "PMID 37335738 full text"}, {"id": "data:geo:GSE152418", "type": "dataset", "label": "GEO GSE152418"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37335738", "type": "paper", "label": "pmid:37335738"}, {"id": "source:pmid:37335738", "type": "manuscript", "label": "PMID 37335738 full text"}, {"id": "data:geo:GSE152418", "type": "dataset", "label": "GEO GSE152418"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37335738", "type": "extraction", "used": ["source:pmid:37335738"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE152418", "type": "accession_resolution", "used": ["data:geo:GSE152418"], "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:37335738", "parent_hash": "sha256:ea97017575fcc13779631a0e5cc22c8fc72bbf18b70e793a87b92b134ebae2ce", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE152418 licence not read", "asset:data:geo:GSE152418 not downloaded", "asset:data:geo:GSE164805 licence not read", "asset:data:geo:GSE164805 not downloaded", "asset:data:geo:GSE198533 licence not read", "asset:data:geo:GSE198533 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["between COVID-19 and Behcet's disease using transcriptome data.", "ractions between the 2 diseases. We used the RNA-seq dataset from the GEO database (GSE152418, GS", "e used a bioinformatics approach to download transcriptomic data from peripheral blood mononuclear cells"], "order_basis": "paper_text_order:39", "id": "assay:1"}, {"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["protein-protein interaction"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}