Identification of the shared mechanisms and common biomarkers between Sjögren's syndrome and atherosclerosis using integrated bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37727764", "kind": "science-record", "revision": 5, "content_hash": "sha256:dff3f09d997968f96eb102ffc94ec7abe0a61b6d989b7fb03bd235f5c3877f4f", "created_at": "2026-11-01T19:02:33Z", "updated_at": "2026-11-01T22:52:45Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of the shared mechanisms and common biomarkers between Sjögren's syndrome and atherosclerosis using integrated bioinformatics analysis.", "doi": "10.3389/fmed.2023.1185303", "pmid": "37727764", "authors": ["Xiaoyi Qi", "Qianwen Huang", "Shijia Wang", "Liangxian Qiu", "Xiongbiao Chen", "Kunfu Ouyang", "Yanjun Chen"], "journal": "Frontiers in medicine", "year": 2023, "abstract": "Background: Sjögren's syndrome (SS) is a chronic autoimmune disease characterized by exocrine and extra-glandular symptoms. The literature indicates that SS is an independent risk factor for atherosclerosis (AS); however, its pathophysiological mechanism remains undetermined. This investigation aimed to elucidate the crosstalk genes and pathways influencing the pathophysiology of SS and AS via bioinformatic analysis of microarray data.\nMethods: Microarray datasets of SS (GSE40611) and AS (GSE28829) were retrieved from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were acquired using R software's \"limma\" packages, and the functions of common DEGs were determined using Gene Ontology and Kyoto Encyclopedia analyses. The protein-protein interaction (PPI) was established using the STRING database. The hub genes were assessed via cytoHubba plug-in and validated by external validation datasets (GSE84844 for SS; GSE43292 for AS). Gene set enrichment analysis (GSEA) and immune infiltration of hub genes were also conducted.\nResults: Eight 8 hub genes were identified using the intersection of four topological algorithms in the PPI network. Four genes (CTSS, IRF8, CYBB, and PTPRC) were then verified as important cross-talk genes between AS and SS with an area under the curve (AUC) ≥0.7. Furthermore, the immune infiltration analysis revealed that lymphocytes and macrophages are essentially linked with the pathogenesis of AS and SS. Moreover, the shared genes were enriched in multiple metabolisms and autoimmune disease-related pathways, as evidenced by GSEA analyses.\nConclusion: This is the first study to explore the common mechanism between SS and AS. Four key genes, including CTSS, CYBB, IRF8, and PTPRC, were associated with the pathogenesis of SS and AS. These hub genes and their correlation with immune cells could be a potential diagnostic and therapeutic target.", "claims": [{"id": "claim-method", "statement": "The “limma” package was used for selecting the DEGs in GSE40611 and GSE28829, with the following criteria: |log2 Fold change (FC)| > 0.5 and value of p <0.01.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37727764", "locator": "sections[4] \"Identification of differentially expressed genes\" paragraph 2", "quote": "The “limma” package was used for selecting the DEGs in GSE40611 and GSE28829, with the following criteria: |log2 Fold change (FC)| > 0.5 and value of p <0.01."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/Supplementary material, further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37727764", "locator": "sections[21] \"Data availability statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/Supplementary material, further inquiries can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Four genes (CTSS, IRF8, CYBB, and PTPRC) were then verified as important cross-talk genes between AS and SS with an area under the curve (AUC) ≥0.7.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37727764", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Four genes (CTSS, IRF8, CYBB, and PTPRC) were then verified as important cross-talk genes between AS and SS with an area under the curve (AUC) ≥0.7."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Four genes (CTSS, IRF8, CYBB, and PTPRC) were then verified as important cross-talk genes between AS and SS with an area under the curve (AUC) ≥0.7.", "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:37727764"], "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:GSE28829"], "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:GSE28829"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37727764", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fmed.2023.1185303", "sha256": "sha256:1f200bb1e07b21bf5d1ce7fa50b0da3579a22ccc337ce87bca48b60ae32b418d", "bytes": 35740, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fmed.2023.1185303", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10506082", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE28829", "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=GSE28829", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE28829", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary material, further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary material, further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM714070", "GSM714071", "GSM714072", "GSM714073", "GSM714074", "GSM714075", "GSM714076", "GSM714077", "GSM714078", "GSM714079", "GSM714080", "GSM714081", "GSM714082", "GSM714083", "GSM714084", "GSM714085", "GSM714086", "GSM714087", "GSM714088", "GSM714089", "GSM714090", "GSM714091", "GSM714092", "GSM714093", "GSM714094", "GSM714095", "GSM714096", "GSM714097", "GSM714098"], "sample_count": 29, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene Expression in early and advanced atherosclerotic plaque from human carotid", "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:GSE28892", "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=GSE28892", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE28892", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary material, further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary material, further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM715841", "GSM715842", "GSM715843", "GSM715844", "GSM715845", "GSM715846", "GSM715847", "GSM715848", "GSM715849", "GSM715850", "GSM715851", "GSM715852", "GSM715853", "GSM715854", "GSM715855", "GSM715856", "GSM715857", "GSM715858", "GSM715859", "GSM715860", "GSM715861", "GSM715862", "GSM715863", "GSM715864", "GSM715865", "GSM715866", "GSM715867", "GSM715868", "GSM715869", "GSM715870", "GSM715871", "GSM715872", "GSM715873", "GSM715874", "GSM715875", "GSM715876", "GSM715877", "GSM715878", "GSM715879", "GSM715880", "GSM715881", "GSM715882", "GSM715883"], "sample_count": 43, "group_sizes": null, "group_sizes_basis": null, "platform": "4134;10333", "taxon": "Mus musculus", "title": "Foxl1-Cre-marked Adult Hepatic Progenitors Have Clonogenic and Bi-Lineage Differentiation Potential", "resolution_checked_at": "2026-11-01T19:09:46Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE40611", "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=GSE40611", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE40611", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary material, further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary material, further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM997850", "GSM997851", "GSM997852", "GSM997853", "GSM997854", "GSM997855", "GSM997856", "GSM997857", "GSM997858", "GSM997859", "GSM997860", "GSM997861", "GSM997862", "GSM997863", "GSM997864", "GSM997865", "GSM997866", "GSM997867", "GSM997868", "GSM997869", "GSM997870", "GSM997871", "GSM997872", "GSM997873", "GSM997874", "GSM997875", "GSM997876", "GSM997877", "GSM997878", "GSM997879", "GSM997880", "GSM997881", "GSM997882", "GSM997883", "GSM997884", "GSM997885", "GSM997886", "GSM997887", "GSM997888", "GSM997889", "GSM997890", "GSM997891", "GSM997892", "GSM997893", "GSM997894", "GSM997895", "GSM997896", "GSM997897", "GSM997898"], "sample_count": 49, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression data of parotid tissue from Primary Sjogren’s Syndrome and controls", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE43292", "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=GSE43292", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE43292", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary material, further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary material, further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1060117", "GSM1060118", "GSM1060119", "GSM1060120", "GSM1060121", "GSM1060122", "GSM1060123", "GSM1060124", "GSM1060125", "GSM1060126", "GSM1060127", "GSM1060128", "GSM1060129", "GSM1060130", "GSM1060131", "GSM1060132", "GSM1060133", "GSM1060134", "GSM1060135", "GSM1060136", "GSM1060137", "GSM1060138", "GSM1060139", "GSM1060140", "GSM1060141", "GSM1060142", "GSM1060143", "GSM1060144", "GSM1060145", "GSM1060146", "GSM1060147", "GSM1060148", "GSM1060149", "GSM1060150", "GSM1060151", "GSM1060152", "GSM1060153", "GSM1060154", "GSM1060155", "GSM1060156", "GSM1060157", "GSM1060158", "GSM1060159", "GSM1060160", "GSM1060161", "GSM1060162", "GSM1060163", "GSM1060164", "GSM1060165", "GSM1060166", "GSM1060167", "GSM1060168", "GSM1060169", "GSM1060170", "GSM1060171", "GSM1060172", "GSM1060173", "GSM1060174", "GSM1060175", "GSM1060176", "GSM1060177", "GSM1060178", "GSM1060179", "GSM1060180"], "sample_count": 64, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Genome-wide expression study of human carotid atheroma", "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:GSE49332", "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=GSE49332", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE49332", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary material, further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary material, further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1197466", "GSM1197467", "GSM1197468"], "sample_count": 3, "group_sizes": null, "group_sizes_basis": null, "platform": "13912", "taxon": "Mus musculus", "title": "Gene expression analysis in  macrophages stimulated 18 h with Adiponectin", "resolution_checked_at": "2026-11-01T19:09:46Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE84844", "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=GSE84844", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE84844", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary material, further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary material, further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2252121", "GSM2252122", "GSM2252123", "GSM2252124", "GSM2252125", "GSM2252126", "GSM2252127", "GSM2252128", "GSM2252129", "GSM2252130", "GSM2252131", "GSM2252132", "GSM2252133", "GSM2252134", "GSM2252135", "GSM2252136", "GSM2252137", "GSM2252138", "GSM2252139", "GSM2252140", "GSM2252141", "GSM2252142", "GSM2252143", "GSM2252144", "GSM2252145", "GSM2252146", "GSM2252147", "GSM2252148", "GSM2252149", "GSM2252150", "GSM2252151", "GSM2252152", "GSM2252153", "GSM2252154", "GSM2252155", "GSM2252156", "GSM2252157", "GSM2252158", "GSM2252159", "GSM2252160", "GSM2252161", "GSM2252162", "GSM2252163", "GSM2252164", "GSM2252165", "GSM2252166", "GSM2252167", "GSM2252168", "GSM2252169", "GSM2252170", "GSM2252171", "GSM2252172", "GSM2252173", "GSM2252174", "GSM2252175", "GSM2252176", "GSM2252177", "GSM2252178", "GSM2252179", "GSM2252180"], "sample_count": 60, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Multi-omics profiling of patients with primary Sjogren's syndrome", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE84884", "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=GSE84884", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE84884", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary material, further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary material, further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2253102", "GSM2253103", "GSM2253104", "GSM2253105"], "sample_count": 4, "group_sizes": null, "group_sizes_basis": null, "platform": "11154", "taxon": "Homo sapiens", "title": "ZSCAN5B and its primate-specific paralogs bind RNA polymerase III genes and extra-TFIIIC (ETC) sites to modulate mitotic progression [SiRNA RNA-Seq data set]", "resolution_checked_at": "2026-11-01T19:09:46Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE28829 not downloaded", "asset:data:geo:GSE28829 licence not read", "asset:data:geo:GSE28892 not downloaded", "asset:data:geo:GSE28892 licence not read", "asset:data:geo:GSE40611 not downloaded", "asset:data:geo:GSE40611 licence not read", "asset:data:geo:GSE43292 not downloaded", "asset:data:geo:GSE43292 licence not read", "asset:data:geo:GSE49332 not downloaded", "asset:data:geo:GSE49332 licence not read", "asset:data:geo:GSE84844 not downloaded", "asset:data:geo:GSE84844 licence not read", "asset:data:geo:GSE84884 not downloaded", "asset:data:geo:GSE84884 licence not read"]}, "analysis": {"state": "partial", "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": "The “limma” package was used for selecting the DEGs in GSE40611 and GSE28829, with the following criteria: |log2 Fold change (FC)| > 0.5 and value of p <0.01."}}, {"id": "method-2", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Wilcoxon"}}, {"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"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "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": ["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": "R1", "reachable": true, "accessions": ["GSE40611", "GSE28829", "GSE28892", "GSE84844", "GSE84884", "GSE43292", "GSE49332"], "resolved_accessions": ["GSE40611", "GSE28829", "GSE28892", "GSE84844", "GSE84884", "GSE43292", "GSE49332"], "statements": ["The original contributions presented in the study are included in the article/Supplementary material, further inquiries can be directed to the corresponding author."], "basis": "The paper names GSE40611, GSE28829, GSE28892, GSE84844, GSE84884, GSE43292, GSE49332 in Gene Expression Omnibus (GEO) database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:37727764", "data:geo:GSE28829"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE28829"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:53:57Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 9873, "completion_tokens": 2522, "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:37727764", "type": "paper", "label": "pmid:37727764"}, {"id": "source:pmid:37727764", "type": "manuscript", "label": "PMID 37727764 full text"}, {"id": "data:geo:GSE28829", "type": "dataset", "label": "GEO GSE28829"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37727764", "type": "paper", "label": "pmid:37727764"}, {"id": "source:pmid:37727764", "type": "manuscript", "label": "PMID 37727764 full text"}, {"id": "data:geo:GSE28829", "type": "dataset", "label": "GEO GSE28829"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37727764", "type": "extraction", "used": ["source:pmid:37727764"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE28829", "type": "accession_resolution", "used": ["data:geo:GSE28829"], "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:37727764", "parent_hash": "sha256:464a3d855b3bb03d5b72e167af864a22f1311d977efb249ab4b5c55630131d12", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE28829 licence not read", "asset:data:geo:GSE28829 not downloaded", "asset:data:geo:GSE28892 licence not read", "asset:data:geo:GSE28892 not downloaded", "asset:data:geo:GSE40611 licence not read", "asset:data:geo:GSE40611 not downloaded", "asset:data:geo:GSE43292 licence not read", "asset:data:geo:GSE43292 not downloaded", "asset:data:geo:GSE49332 licence not read", "asset:data:geo:GSE49332 not downloaded", "asset:data:geo:GSE84844 licence not read", "asset:data:geo:GSE84844 not downloaded", "asset:data:geo:GSE84884 licence not read", "asset:data:geo:GSE84884 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "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": 0.99, "evidence": ["y of SS and AS via bioinformatic analysis of microarray data. Methods: Microarray datasets of SS (GS", "rmatic analysis of microarray data. Methods: Microarray datasets of SS (GSE40611) and AS (GSE28829)"], "order_basis": "paper_text_order:529", "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": ["The “limma” package was used for selecting the DEGs in GSE40611 and GSE28829, with the following criteria: |log2 Fold change (FC)| > 0.5 and value of p <0.01."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}