Integrated Analysis of Multiple Microarray Studies to Identify Core Gene-Expression Signatures Involved in Tubulointerstitial Injury in Diabetic Nephropathy.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35592524", "kind": "science-record", "revision": 5, "content_hash": "sha256:94234c52397f34f1e43d4f31d0bb6fe16cc7c92eac2c2c2ab3395385e67a8e16", "created_at": "2026-11-01T18:14:29Z", "updated_at": "2026-11-01T22:49:05Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated Analysis of Multiple Microarray Studies to Identify Core Gene-Expression Signatures Involved in Tubulointerstitial Injury in Diabetic Nephropathy.", "doi": "10.1155/2022/9554658", "pmid": "35592524", "authors": ["Huandi Zhou", "Zhifen Yang", "Lin Mu", "Yonghong Shi"], "journal": "BioMed research international", "year": 2022, "abstract": "Diabetic nephropathy is a leading cause of end-stage renal disease in both developed and developing countries. It is lack of specific diagnosis, and the pathogenesis remains unclarified in diabetic nephropathy, following the unsatisfactory effects of existing treatments. Therefore, it is very meaningful to find biomarkers with high specificity and potential targets. Two datasets, GSE30529 and GSE47184 from GEO based on diabetic nephropathy tubular samples, were downloaded and merged after batch effect removal. A total of 545 different expression genes screened with log2FC > 0.5 were weighted gene coexpression correlation network analysis, and green module and blue module were identified. The results of KEGG analyses both in green module and GSEA analysis showed the same two enriched pathway, focal adhesion and viral myocarditis. Based on the intersection among WGCNA focal adhesion/Viral myocarditis, GSEA focal adhesion/viral myocarditis, and PPI network, 17 core genes, ACTN1, CAV1, PRKCB, PDGFRA, COL1A2, COL6A3, RHOA, VWF, FN1, HLA-F, HLA-DPB1, ITGB2, HLA-DRA, HLA-DMA, HLA-DPA1, HLA-B, and HLA-DMB, were identified as potential biomarkers in diabetic tubulointerstitial injury and were further validated externally for expression at GSE99325 and GSE104954 and clinical feature at nephroseq V5 online platform. CMap analysis suggested that two compounds, LY-294002 and bufexamac, may be new insights for therapeutics of diabetic tubulointerstitial injury. Conclusively, it was raised that a series of core genes may be as potential biomarkers for diagnosis and two prospective compounds.", "claims": [{"id": "claim-method", "statement": "After batch normalization, 545 DEGs were filtered out by the limma R package (adjusted P < 0.05 and |log2FC| > 0.5), in which 375 genes were upregulated, and 170 were downregulated (Figure 2(e)).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35592524", "locator": "sections[13] \"3.1. Identification of DEGs Specifically Involved in Tubulointerstitial Injury in DN\" paragraph 4", "quote": "After batch normalization, 545 DEGs were filtered out by the limma R package (adjusted P < 0.05 and |log2FC| > 0.5), in which 375 genes were upregulated, and 170 were downregulated (Figure 2(e))."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated during and/or analyzed during the current study are presented in the main file. Additional data are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35592524", "locator": "sections[23] \"Data Availability\" paragraph 2", "quote": "The datasets generated during and/or analyzed during the current study are presented in the main file. 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Identification of DEGs Specifically Involved in Tubulointerstitial Injury in DN\" paragraph 4", "quote": "After batch normalization, 545 DEGs were filtered out by the limma R package (adjusted P < 0.05 and |log2FC| > 0.5), in which 375 genes were upregulated, and 170 were downregulated (Figure 2(e))."}, {"asset": "source:pmid:35592524", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "A total of 545 different expression genes screened with log2FC > 0.5 were weighted gene coexpression correlation network analysis, and green module and blue module were identified."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "After merging two GEO datasets, 545 DEGs were identified and analyzed with weighted gene coexpression network analysis, which identified green and blue modules.", "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:35592524"], "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. 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE30529", "GSE47184", "GSE99325", "GSE104954"], "resolved_accessions": ["GSE30529", "GSE47184", "GSE99325", "GSE104954"], "statements": ["The datasets generated during and/or analyzed during the current study are presented in the main file. Additional data are available from the corresponding author on reasonable request."], "basis": "The paper names GSE30529, GSE47184, GSE99325, GSE104954 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:35592524", "data:geo:GSE104954"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE104954"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:46:50Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 18946, "completion_tokens": 2205, "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:35592524", "type": "paper", "label": "pmid:35592524"}, {"id": "source:pmid:35592524", "type": "manuscript", "label": "PMID 35592524 full text"}, {"id": "data:geo:GSE104954", "type": "dataset", "label": "GEO GSE104954"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35592524", "type": "paper", "label": "pmid:35592524"}, {"id": "source:pmid:35592524", "type": "manuscript", "label": "PMID 35592524 full text"}, {"id": "data:geo:GSE104954", "type": "dataset", "label": "GEO GSE104954"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35592524", "type": "extraction", "used": ["source:pmid:35592524"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE104954", "type": "accession_resolution", "used": ["data:geo:GSE104954"], "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:35592524", "parent_hash": "sha256:1e594782264a7fe0d9de6e05697ea744c914a14d378c6e43bd88e5daf6f39914", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE104954 licence not read", "asset:data:geo:GSE104954 not downloaded", "asset:data:geo:GSE30529 licence not read", "asset:data:geo:GSE30529 not downloaded", "asset:data:geo:GSE47184 licence not read", "asset:data:geo:GSE47184 not downloaded", "asset:data:geo:GSE99325 licence not read", "asset:data:geo:GSE99325 not downloaded", "execution.not_run", "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": ["Integrated Analysis of Multiple Microarray Studies to Identify Core Gene-Expression Sig"], "order_basis": "paper_text_order:0", "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": ["After batch normalization, 545 DEGs were filtered out by the limma R package (adjusted P < 0.05 and |log2FC| > 0.5), in which 375 genes were upregulated, and 170 were downregulated (Figure 2(e))."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}