Bioinformatic analysis, clinical implications and experimental validation of ferroptosis-related feature gene in IgA nephropathy: focus on DUSP1.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40852352", "kind": "science-record", "revision": 4, "content_hash": "sha256:0454a5d5a90cb41bf9a02200b153c5cee68d2625b68deffacde6a55db1e93913", "created_at": "2026-11-01T20:30:57Z", "updated_at": "2026-11-01T22:57:04Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatic analysis, clinical implications and experimental validation of ferroptosis-related feature gene in IgA nephropathy: focus on DUSP1.", "doi": "10.3389/fmed.2025.1612200", "pmid": "40852352", "authors": ["Tingting Liu", "Tingting Pan", "Mingxin Chang", "Shaojie Fu", "Hongzhao Xu", "Hao Wu", "Zhonggao Xu", "Yanli Cheng"], "journal": "Frontiers in medicine", "year": 2025, "abstract": "Background: Immunoglobulin A nephropathy (IgAN), recognized as the leading cause of primary glomerular disease worldwide, continues to present unresolved complexities in its underlying pathogenic mechanisms. Emerging evidence underscores ferroptosis, an iron-mediated regulated cell death pathway driven by the accumulation of lipid peroxides, as a potential contributor to various pathological conditions. Despite growing interest in this field, the exact molecular pathways governing ferroptosis activation in IgAN progression remain incompletely understood and require systematic investigation. The aim of this study was to identify ferroptosis-related feature gene (FFG) for the potential diagnosis of IgAN and to investigate its relationship with renal immune cell infiltration.\nMethods: Renal tissue microarray datasets (GSE93798, GSE104948, GSE99339) from IgAN patients and normal controls were retrieved from GEO database. The ferroptosis-related genes were obtained from the Ferrb database. Machine learning algorithms (LASSO, SVM-RFE, random forest) were employed to screen FFGs. The findings were validated in an IgAN mouse model using immunohistochemistry and western blotting. Gene set enrichment analysis (GSEA) was conducted to explore the underlying mechanism of FFG in IgAN. Immune cell infiltration characteristics were also analyzed vis CIBERSORT algorithm.\nResults: A total of 180 ferroptosis-related differentially expressed genes were identified in IgAN. Among them, dual specificity phosphatase 1 (DUSP1) was screened as FFG by three machine learning algorithms. DUSP1 exhibited significant downregulation in renal tissues of both IgAN patients and mice. Enhanced transcriptional abundance demonstrated significant positive associations with ferroptosis-associated biomarkers glutathione peroxidase-4 (GPX4) and cystine/glutamate antiporter (SLC7A11/xCT), while displaying an inverse relationship with acyl-CoA synthetase long-chain isoform 4 (ACSL4) expression. GSEA further identified DUSP1's functional enrichment in critical signaling networks, particularly mitogen-activated protein kinase (MAPK) cascades, ERBB receptor tyrosine kinase pathways, and Janus kinase-signal transducer (JAK-STAT) transduction mechanisms. Immunoinfiltration analysis demonstrated increased infiltration of T follicular helper cells, activated NK cells, and M1 macrophages in the renal tissues of IgAN patients, with DUSP1 expression showing negative correlations with these proinflammatory cell types.\nConclusion: Our research successfully identified DUSP1 as a ferroptosis-related biomarker in IgAN patients, and explored its potential mechanism in the pathogenesis of IgAN and its potential relationship with immune cell infiltration. These findings are of great significance for the diagnosis and prospective treatment strategies for IgAN patients.", "claims": [{"id": "claim-method", "statement": "The “limma” [version 3.56.2] R package was conducted to assess the differences in gene expression data (20). To control the proportion of false positives due to multiple testing, false discovery rate (FDR) correction was also applied.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40852352", "locator": "sections[4] \"Identification of ferroptosis-related differential expressed genes\" paragraph 2", "quote": "The “limma” [version 3.56.2] R package was conducted to assess the differences in gene expression data (20). To control the proportion of false positives due to multiple testing, false discovery rate (FDR) correction was also applied."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The chip data analyzed in this study were obtained from Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo/). GSE93798 was downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE93798, GSE104948 was downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE104948, and GSE99339 was downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE99339.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40852352", "locator": "sections[30] \"Data availability statement\" paragraph 2", "quote": "The chip data analyzed in this study were obtained from Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo/). GSE93798 was downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE93798, GSE104948 was downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE104948, and GSE99339 was downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE99339."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Differential analyses of the data were performed with statistical significance of FDR-p value <0.05, and a total of 180 FDEGs were identified, including 98 downregulated and 82 upregulated genes (Supplementary Table 1).", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "Differential analyses of the data were performed with statistical significance of FDR-p value <0.05, and a total of 180 FDEGs were identified, including 98 downregulated and 82 upregulated genes (Supplementary Table 1)."}, "evidence": [{"asset": "source:pmid:40852352", "locator": "sections[18] \"Identification of ferroptosis-related differential expressed genes in IgAN\" paragraph 2", "quote": "Differential analyses of the data were performed with statistical significance of FDR-p value <0.05, and a total of 180 FDEGs were identified, including 98 downregulated and 82 upregulated genes (Supplementary Table 1)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Differential analyses of the data were performed with statistical significance of FDR-p value <0.05, and a total of 180 FDEGs were identified, including 98 downregulated and 82 upregulated genes (Supplementary Table 1).", "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:40852352"], "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:GSE104948"], "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": {"fdr_threshold": "he limma R package with false discovery rate correction"}, "inputs": ["data:geo:GSE104948"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40852352", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fmed.2025.1612200", "sha256": "sha256:d06f43eb6863e7fc87f29a3854e9aba035ae965052979b28cb3a5f5fbf4f4f94", "bytes": 50012, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fmed.2025.1612200", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12367746", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE104948", "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=GSE104948", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE104948", "version": null, "note": "The chip data analyzed in this study were obtained from Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo/). GSE93798 was downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE93798, GSE104948 was downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE104948, and GSE99339 was downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE99339.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The chip data analyzed in this study were obtained from Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo/). 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GSE93798 was downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE93798, GSE104948 was downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE104948, and GSE99339 was downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE99339.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The chip data analyzed in this study were obtained from Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo/). GSE93798 was downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE93798, GSE104948 was downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE104948, and GSE99339 was downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE99339.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2462533", "GSM2462534", "GSM2462535", "GSM2462536", "GSM2462537", "GSM2462538", "GSM2462539", "GSM2462540", "GSM2462541", "GSM2462542", "GSM2462543", "GSM2462544", "GSM2462545", "GSM2462546", "GSM2462547", "GSM2462548", "GSM2462549", "GSM2462550", "GSM2462551", "GSM2462552", "GSM2462553", "GSM2462554", "GSM2462555", "GSM2462556", "GSM2462557", "GSM2462558", "GSM2462559", "GSM2462560", "GSM2462561", "GSM2462562", "GSM2462563", "GSM2462564", "GSM2462565", "GSM2462566", "GSM2462567", "GSM2462568", "GSM2462569", "GSM2462570", "GSM2462571", "GSM2462572", "GSM2462573", "GSM2462574"], "sample_count": 42, "group_sizes": null, "group_sizes_basis": null, "platform": "22945", "taxon": "Homo sapiens", "title": "Transcriptomic and proteomic profiling reveal insights of mesangial cell function in patients with IgA Nephropathy", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE99339", "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=GSE99339", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE99339", "version": null, "note": "The chip data analyzed in this study were obtained from Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo/). GSE93798 was downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE93798, GSE104948 was downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE104948, and GSE99339 was downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE99339.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The chip data analyzed in this study were obtained from Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo/). GSE93798 was downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE93798, GSE104948 was downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE104948, and GSE99339 was downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE99339.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2642291", "GSM2642292", "GSM2642293", "GSM2642294", "GSM2642295", "GSM2642296", "GSM2642297", "GSM2642298", "GSM2642299", "GSM2642300", "GSM2642301", "GSM2642302", "GSM2642303", "GSM2642304", "GSM2642305", "GSM2642306", "GSM2642307", "GSM2642308", "GSM2642309", "GSM2642310", "GSM2642311", "GSM2642312", "GSM2642313", "GSM2642314", "GSM2642315", "GSM2642316", "GSM2642317", "GSM2642318", "GSM2642319", "GSM2642320", "GSM2642321", "GSM2642322", "GSM2642323", "GSM2642324", "GSM2642325", "GSM2642326", "GSM2642327", "GSM2642328", "GSM2642329", "GSM2642330", "GSM2642331", "GSM2642332", "GSM2642333", "GSM2642334", "GSM2642335", "GSM2642336", "GSM2642337", "GSM2642338", "GSM2642339", "GSM2642340", "GSM2642341", "GSM2642342", "GSM2642343", "GSM2642344", "GSM2642345", "GSM2642346", "GSM2642347", "GSM2642348", "GSM2642349", "GSM2642350", "GSM2642351", "GSM2642352", "GSM2642353", "GSM2642354", "GSM2642355", "GSM2642356", "GSM2642357", "GSM2642358", "GSM2642359", "GSM2642360", "GSM2642361", "GSM2642362", "GSM2642363", "GSM2642364", "GSM2642365", "GSM2642366", "GSM2642367", "GSM2642368", "GSM2642369", "GSM2642370", "GSM2642371", "GSM2642372", "GSM2642373", "GSM2642374", "GSM2642375", "GSM2642376", "GSM2642377", "GSM2642378", "GSM2642379", "GSM2642380", "GSM2642381", "GSM2642382", "GSM2642383", "GSM2642384", "GSM2642385", "GSM2642386", "GSM2642387", "GSM2642388", "GSM2642389", "GSM2642390", "GSM2642391", "GSM2642392", "GSM2642393", "GSM2642394", "GSM2642395", "GSM2642396", "GSM2642397", "GSM2642398", "GSM2642399", "GSM2642400", "GSM2642401", "GSM2642402", "GSM2642403", "GSM2642404", "GSM2642405", "GSM2642406", "GSM2642407", "GSM2642408", "GSM2642409", "GSM2642410", "GSM2642411", "GSM2642412", "GSM2642413", "GSM2642414", "GSM2642415", "GSM2642416", "GSM2642417", "GSM2642418", "GSM2642419", "GSM2642420", "GSM2642421", "GSM2642422", "GSM2642423", "GSM2642424", "GSM2642425", "GSM2642426", "GSM2642427", "GSM2642428", "GSM2642429", "GSM2642430", "GSM2642431", "GSM2642432", "GSM2642433", "GSM2642434", "GSM2642435", "GSM2642436", "GSM2642437", "GSM2642438", "GSM2642439", "GSM2642440", "GSM2642441", "GSM2642442", "GSM2642443", "GSM2642444", "GSM2642445", "GSM2642446", "GSM2642447", "GSM2642448", "GSM2642449", "GSM2642450", "GSM2642451", "GSM2642452", "GSM2642453", "GSM2642454", "GSM2642455", "GSM2642456", "GSM2642457", "GSM2642458", "GSM2642459", "GSM2642460", "GSM2642461", "GSM2642462", "GSM2642463", "GSM2642464", "GSM2642465", "GSM2642466", "GSM2642467", "GSM2642468", "GSM2642469", "GSM2642470", "GSM2642471", "GSM2642472", "GSM2642473", "GSM2642474", "GSM2642475", "GSM2642476", "GSM2642477"], "sample_count": 187, "group_sizes": null, "group_sizes_basis": null, "platform": "19109;19184", "taxon": "Homo sapiens", "title": "Transcriptome-based network analysis reveals renal cell type-specific dysregulation of hypoxia-associated transcripts [glomeruli]", "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:GSE104948 not downloaded", "asset:data:geo:GSE104948 licence not read", "asset:data:geo:GSE93798 not downloaded", "asset:data:geo:GSE93798 licence not read", "asset:data:geo:GSE99339 not downloaded", "asset:data:geo:GSE99339 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": {"fdr_threshold": "he limma R package with false discovery rate correction"}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The “limma” [version 3.56.2] R package was conducted to assess the differences in gene expression data (20). To control the proportion of false positives due to multiple testing, false discovery rate (FDR) correction was also applied."}}, {"id": "method-2", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "ANOVA"}}, {"id": "method-3", "family": "machine_learning", "specific": "random_forest", "label": "Machine learning", "dsl_operations": [], "missing_operations": ["machine_learning_random_forest"], "expressible": false, "parameters": {}, "data_shapes": ["labelled_feature_matrix"], "evidence": {"score": 0.7, "band": "medium", "quote": "random forest"}}, {"id": "method-4", "family": "machine_learning", "specific": "support_vector_machine", "label": "Machine learning", "dsl_operations": ["train_classifier", "cross_validate", "roc_auc"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["labelled_feature_matrix"], "evidence": {"score": 0.7, "band": "medium", "quote": "SVM"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "bootstrap_mean_difference", "expected_value": 0.05, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "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": ["GSE93798", "GSE104948", "GSE99339"], "resolved_accessions": ["GSE93798", "GSE104948", "GSE99339"], "statements": ["The chip data analyzed in this study were obtained from Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo/). GSE93798 was downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE93798, GSE104948 was downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE104948, and GSE99339 was downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE99339."], "basis": "The paper names GSE93798, GSE104948, GSE99339 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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:40852352", "data:geo:GSE104948"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE104948"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T20:00:11Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 12672, "completion_tokens": 1706, "cached_tokens": 264}}, "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:40852352", "type": "paper", "label": "pmid:40852352"}, {"id": "source:pmid:40852352", "type": "manuscript", "label": "PMID 40852352 full text"}, {"id": "data:geo:GSE104948", "type": "dataset", "label": "GEO GSE104948"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:40852352", "type": "paper", "label": "pmid:40852352"}, {"id": "source:pmid:40852352", "type": "manuscript", "label": "PMID 40852352 full text"}, {"id": "data:geo:GSE104948", "type": "dataset", "label": "GEO GSE104948"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-40852352", "type": "extraction", "used": ["source:pmid:40852352"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE104948", "type": "accession_resolution", "used": ["data:geo:GSE104948"], "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:40852352", "parent_hash": "sha256:33079516b15224c40e5b12ea1788f9a610bc2c4937403a5c71d5af2eb76b4cef", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE104948 licence not read", "asset:data:geo:GSE104948 not downloaded", "asset:data:geo:GSE93798 licence not read", "asset:data:geo:GSE93798 not downloaded", "asset:data:geo:GSE99339 licence not read", "asset:data:geo:GSE99339 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": 0.93, "evidence": ["une cell infiltration. Methods: Renal tissue microarray datasets (GSE93798, GSE104948, GSE99339) fro"], "order_basis": "paper_text_order:907", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["FFGs. The findings were validated in an IgAN mouse model using immunohistochemistry and western blott", "FFGs. The findings were validated in an IgAN mouse model using immunohistochemistry and western", "the 6th and 8th weeks). Following this, the mice were humanely euthanized, and samples of blood, u", "analysis of CD3+ and CD4+ T cell subsets in mouse kidney tissue. Data were expressed as mean ±"], "order_basis": "paper_text_order:1230", "id": "assay:2"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["were validated in an IgAN mouse model using immunohistochemistry and western blotting. Gene set enrichment an"], "order_basis": "paper_text_order:1249", "id": "assay:3"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["N mouse model using immunohistochemistry and western blotting. Gene set enrichment analysis (GSEA) was con"], "order_basis": "paper_text_order:1273", "id": "assay:4"}, {"role": "data_generation", "definition_id": "flow_cytometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["—all key processes in renal pathophysiology. Flow cytometry analysis of immune cell infiltration in rena", "y validate the immune infiltration findings, flow cytometry analysis on renal tissues from both IgAN and", "ar helper cells in renal tissue during IgAN. Flow cytometry analysis. Flow cytometry analysis of CD3+ an", "tissue during IgAN. Flow cytometry analysis. Flow cytometry analysis of CD3+ and CD4+ T cell subsets in"], "order_basis": "paper_text_order:7166", "id": "assay:5"}, {"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” [version 3.56.2] R package was conducted to assess the differences in gene expression data (20). To control the proportion of false positives due to multiple testing, false discovery rate (FDR) correction was also applied."], "order_basis": "consumes_earlier_output", "id": "assay:6"}]}