Identification and Clinical Correlation Analysis of IFI44 in Systemic Lupus Erythematosus Combined with Bioinformatics and Immune Infiltration Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37547125", "kind": "science-record", "revision": 4, "content_hash": "sha256:eca527a6fb711101ad14bdaaaa4779f0f88cf699b7b800802383c4cd7461263b", "created_at": "2026-11-01T19:02:19Z", "updated_at": "2026-11-01T22:52:27Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and Clinical Correlation Analysis of IFI44 in Systemic Lupus Erythematosus Combined with Bioinformatics and Immune Infiltration Analysis.", "doi": "10.2147/JIR.S419880", "pmid": "37547125", "authors": ["Yuan Wang", "Chengfeng Ma", "Zhanbing Ma", "Mengyi Yang", "Jing Pu", "Xiuhui Ma", "Xi Wu", "Liang Peng", "Zhenghao Huo", "Jie Dang"], "journal": "Journal of inflammation research", "year": 2023, "abstract": "Purpose: Systemic lupus erythematosus (SLE) is a chronic autoimmune disease that can cause systemic damage to multiple organs. This study aims to analyze the value and function of IFI44 in the diagnosis and pathology of SLE by bioinformatics and immune infiltration analysis.\nPatients and Methods: GSE49454 and GSE65391 of SLE were obtained from the GEO dataset, and R software was employed to identify DEGs and investigate their functions. The PPI network was utilized to identify hub genes associated with SLE. CIBERSORT was used to assess differences in immune cell infiltration in SLE patients and controls. ROC curve analysis was performed to evaluate the diagnostic value of IFI44 in SLE. The expression of IFI44 in PBMCs was detected by RT-qPCR, and the correlation between IFI44 expression and SLE-related clinical indicators was analyzed.\nResults: A total of 65 DEGs were identified from the GSE49454 and GSE65391 databases. Through PPI analysis, IFI44 and RSAD2 were identified as significantly aberrantly expressed in SLE patients. SLE patients and controls showed a significant difference in the proportion of immune cell infiltration. IFI44 expression was positively correlated with activated DCs, monocytes, PCs, neutrophils, and activated memory CD4+T cells, while negatively correlated with M0 and CD8+T cells. The expression of IFI44 was significantly higher in SLE patients (P<0.01), especially in male patients (P=0.0376). ROC curve analysis demonstrated that IFI44 had a high diagnostic value for SLE. Correlation analysis indicated that IFI44 expression was correlated with levels of RBC, HGB, HCT, IgA, ESR, UPRO, C3, C4, and ENA in SLE patients.\nConclusion: IFI44 may play a role in the pathogenesis of SLE by influencing the immune microenvironment of SLE patients, and thus has the potential to serve as a diagnostic marker and therapeutic target for SLE.", "claims": [{"id": "claim-method", "statement": "The “limma” package was utilized to identify DEGs in SLE patients compared to healthy controls.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37547125", "locator": "sections[4] \"Identification of DEGs\" paragraph 2", "quote": "The “limma” package was utilized to identify DEGs in SLE patients compared to healthy controls."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Finally, GSE49454 and GSE65391 were obtained, which consist of 157 and 924 SLE patients, and 20 and 72 healthy control samples, respectively.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37547125", "locator": "sections[3] \"Access to GEO Datasets\" paragraph 2", "quote": "Finally, GSE49454 and GSE65391 were obtained, which consist of 157 and 924 SLE patients, and 20 and 72 healthy control samples, respectively."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 65 DEGs were identified from the GSE49454 and GSE65391 databases.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37547125", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 65 DEGs were identified from the GSE49454 and GSE65391 databases."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 65 DEGs were identified from the GSE49454 and GSE65391 databases.", "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:37547125"], "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:GSE49454"], "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:GSE49454"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37547125", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/JIR.S419880", "sha256": 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samples, respectively.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Finally, GSE49454 and GSE65391 were obtained, which consist of 157 and 924 SLE patients, and 20 and 72 healthy control samples, respectively.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1199352", "GSM1199353", "GSM1199354", "GSM1199355", "GSM1199356", "GSM1199357", "GSM1199358", "GSM1199359", "GSM1199360", "GSM1199361", "GSM1199362", "GSM1199363", "GSM1199364", "GSM1199365", "GSM1199367", "GSM1199369", "GSM1199373", "GSM1199376", "GSM1199379", "GSM1199381", "GSM1199384", "GSM1199386", "GSM1199388", "GSM1199391", "GSM1199394", "GSM1199396", "GSM1199398", "GSM1199399", "GSM1199400", "GSM1199401", "GSM1199402", "GSM1199403", "GSM1199404", "GSM1199405", "GSM1199406", "GSM1199407", "GSM1199408", "GSM1199409", "GSM1199410", "GSM1199411", "GSM1199412", "GSM1199413", "GSM1199414", "GSM1199415", "GSM1199416", "GSM1199417", 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identify dynamic type I and type II interferon transcriptional signatures in adult SLE patients", "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:GSE65391", "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=GSE65391", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE65391", "version": null, "note": "Finally, GSE49454 and GSE65391 were obtained, which consist of 157 and 924 SLE patients, and 20 and 72 healthy control samples, respectively.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Finally, GSE49454 and GSE65391 were obtained, which consist of 157 and 924 SLE patients, and 20 and 72 healthy control samples, respectively.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1594219", "GSM1594220", "GSM1594221", "GSM1594222", "GSM1594223", "GSM1594224", "GSM1594225", "GSM1594226", "GSM1594227", "GSM1594228", "GSM1594229", "GSM1594230", "GSM1594231", "GSM1594232", "GSM1594233", "GSM1594234", "GSM1594235", "GSM1594236", "GSM1594237", "GSM1594238", "GSM1594239", "GSM1594240", "GSM1594241", "GSM1594244", "GSM1594247", "GSM1594250", "GSM1594253", "GSM1594254", "GSM1594255", "GSM1594256", "GSM1594257", "GSM1594258", "GSM1594259", "GSM1594260", "GSM1594261", "GSM1594262", "GSM1594263", "GSM1594264", "GSM1594265", "GSM1594266", "GSM1594267", "GSM1594268", "GSM1594269", "GSM1594270", "GSM1594271", "GSM1594272", "GSM1594273", "GSM1594274", "GSM1594275", "GSM1594276", "GSM1594277", "GSM1594278", "GSM1594279", "GSM1594280", "GSM1594281", "GSM1594282", "GSM1594283", "GSM1594284", "GSM1594285", "GSM1594286", "GSM1594287", "GSM1594288", "GSM1594289", "GSM1594290", 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"GSM1595072", "GSM1595073", "GSM1595074", "GSM1595075", "GSM1595076", "GSM1595077", "GSM1595078", "GSM1595079", "GSM1595080", "GSM1595081", "GSM1595082", "GSM1595083", "GSM1595084", "GSM1595085", "GSM1595086", "GSM1595087", "GSM1595088", "GSM1595089", "GSM1595090", "GSM1595091", "GSM1595092", "GSM1595093", "GSM1595094", "GSM1595095", "GSM1595096", "GSM1595097", "GSM1595098", "GSM1595099", "GSM1595100", "GSM1595101", "GSM1595102", "GSM1595103", "GSM1595104", "GSM1595105", "GSM1595106", "GSM1595107", "GSM1595108", "GSM1595109", "GSM1595110", "GSM1595111", "GSM1595112", "GSM1595113", "GSM1595114", "GSM1595115", "GSM1595116", "GSM1595117", "GSM1595118", "GSM1595119", "GSM1595120", "GSM1595121", "GSM1595122", "GSM1595123", "GSM1595124", "GSM1595125", "GSM1595126", "GSM1595127", "GSM1595128", "GSM1595129", "GSM1595130", "GSM1595131", "GSM1595132", "GSM1595133", "GSM1595134", "GSM1595135", "GSM1595136", "GSM1595137", "GSM1595138", "GSM1595139", "GSM1595140", "GSM1595141", "GSM1595142", "GSM1595143", "GSM1595144", "GSM1595145", "GSM1595146", "GSM1595147", "GSM1595148", "GSM1595149", "GSM1595150", "GSM1595151", "GSM1595152", "GSM1595153", "GSM1595154", "GSM1595155", "GSM1595156", "GSM1595157", "GSM1595158", "GSM1595159", "GSM1595160", "GSM1595161", "GSM1595162", "GSM1595163", "GSM1595164", "GSM1595165", "GSM1595166", "GSM1595167", "GSM1595168", "GSM1595169", "GSM1595170", "GSM1595171", "GSM1595172", "GSM1595173", "GSM1595174", "GSM1595175", "GSM1595176", "GSM1595177", "GSM1595178", "GSM1595179", "GSM1595180", "GSM1595181", "GSM1595182", "GSM1595183", "GSM1595184", "GSM1595185", "GSM1595186", "GSM1595187", "GSM1595188", "GSM1595189", "GSM1595190", "GSM1595191", "GSM1595192", "GSM1595193", "GSM1595194", "GSM1595195", "GSM1595196", "GSM1595197", "GSM1595198", "GSM1595199", "GSM1595200", "GSM1595201", "GSM1595202", "GSM1595203", "GSM1595204", "GSM1595205", "GSM1595206", "GSM1595207", "GSM1595208", "GSM1595209", "GSM1595210", "GSM1595211", "GSM1595212", "GSM1595213", "GSM1595214", "GSM1595215", "GSM1595216", "GSM1595217", "GSM1595218", "GSM1595219", "GSM1595220", "GSM1595221", "GSM1595222"], "sample_count": 996, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Longitudinal transcriptional pediatric SLE study with clinical parameters", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE49454 not downloaded", "asset:data:geo:GSE49454 licence not read", "asset:data:geo:GSE65391 not downloaded", "asset:data:geo:GSE65391 licence not read"]}, "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": "The “limma” package was utilized to identify DEGs in SLE patients compared to healthy controls."}}, {"id": "method-2", "family": "correlation_analysis", "specific": "spearman", "label": "Correlation analysis", "dsl_operations": ["spearman_rho"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Spearman 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": "PPI"}}, {"id": "method-4", "family": "diagnostic_evaluation", "specific": "roc", "label": "Diagnostic test evaluation", "dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["reference_standard_and_test"], "evidence": {"score": 0.7, "band": "medium", "quote": "ROC curve"}}], "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": "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": ["GSE49454", "GSE65391"], "resolved_accessions": ["GSE49454", "GSE65391"], "statements": ["Finally, GSE49454 and GSE65391 were obtained, which consist of 157 and 924 SLE patients, and 20 and 72 healthy control samples, respectively."], "basis": "The paper names GSE49454, GSE65391 in 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:37547125", "data:geo:GSE49454"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE49454"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:48:54Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 9600, "completion_tokens": 1316, "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:37547125", "type": "paper", "label": "pmid:37547125"}, {"id": "source:pmid:37547125", "type": "manuscript", "label": "PMID 37547125 full text"}, {"id": "data:geo:GSE49454", "type": "dataset", "label": "GEO GSE49454"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37547125", "type": "paper", "label": "pmid:37547125"}, {"id": "source:pmid:37547125", "type": "manuscript", "label": "PMID 37547125 full text"}, {"id": "data:geo:GSE49454", "type": "dataset", "label": "GEO GSE49454"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37547125", "type": "extraction", "used": ["source:pmid:37547125"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE49454", "type": "accession_resolution", "used": ["data:geo:GSE49454"], "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:37547125", "parent_hash": "sha256:73c6e428cc4d0517181f70e56205f1252214ec088124f69600b06b5e7122477a", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE49454 licence not read", "asset:data:geo:GSE49454 not downloaded", "asset:data:geo:GSE65391 licence not read", "asset:data:geo:GSE65391 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["expression of IFI44 in PBMCs was detected by RT-qPCR, and the correlation between IFI44 expressio", "ression of IFI44 in PBMCs was detected by RT-qPCR, and the correlation between IFI44 expressio", "potential role of IFI44 in SLE pathogenesis. RT-qPCR was conducted to analyze the expression of I", "ential role of IFI44 in SLE pathogenesis. RT-qPCR was conducted to analyze the expression of I"], "order_basis": "paper_text_order:852", "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 utilized to identify DEGs in SLE patients compared to healthy controls."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}