Identification of transcription factors related to diabetic tubulointerstitial injury.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36978091", "kind": "science-record", "revision": 2, "content_hash": "sha256:ce83962234e594b70036e66be90afa01134764205a66f01eaf5b9b5ec27655d4", "created_at": "2026-11-01T19:01:38Z", "updated_at": "2026-11-01T21:30:27Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of transcription factors related to diabetic tubulointerstitial injury.", "doi": "10.1186/s12967-023-04069-8", "pmid": "36978091", "authors": ["Jialu Liu", "Guangzhong Duan", "Wenxia Yang", "Shumin Zhang", "Fuyou Liu", "Youming Peng", "Lin Sun", "Yu Liu", "Li Xiao"], "journal": "Journal of translational medicine", "year": 2023, "abstract": "BACKGROUND: Diabetic nephropathy (DN) is a main cause of chronic renal failure. Despite decades of extensive study, the molecular mechanisms underlying diabetic tubulointerstitial injury remain unclear. We aim to identify key transcription factor genes involved in diabetic tubulointerstitial injury.\nMETHODS: A microarray dataset (GSE30122) from Gene Expression Omnibus (GEO) was downloaded. A total of 38 transcription factor genes based on 166 differentially expressed genes (DEGs) were identified by UCSC_TFBS.\nRESULTS: The regulatory network showed connections between the top 10 transcription factors and their target DEGs. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of targeted DEGs indicated that extracellular space, extracellular exosome, cell surface and complement and coagulation cascades were most significantly enriched. Utilizing Nephroseq v5 online platform, the mRNA expression pattern analysis of transcription factor genes demonstrated that mRNA expression of CDC5, CEBPA, FAC1, HFH1, IRF1, NFE2 and TGIF1 increased in renal tubulointerstitium of DN patients compared with normal controls while that of CEBPB and FOXO4 decreased in renal tubulointerstitium of DN patients compared with normal controls. Correlation analysis between mRNA expression of transcription factor genes in renal tubulointerstitium and clinical features showed that AP1, BACH1, CDC5, FAC1, FOXD1, FOXJ2, FOXO1, FOXO4, HFH1, IRF1, POU3F2, SOX5, SOX9, RSRFC4, S8 and TGIF1 may be related to diabetic tubulointerstitial injury.\nCONCLUSIONS: (1) CDC5, FAC1, FOXO4, HFH1, IRF1 and TGIF1 may be key transcription factor genes. (2)Transcription factors involved in diabetic tubulointerstitial injury may become prospective targets for diagnosis and treatment of DN.", "claims": [{"id": "claim-method", "statement": "Also, Pearson correlation analysis between transcription factor genes and glomerular filtration rate (GFR) [17, 25], serum creatine level (SCR) [24, 25], proteinuria [25], body weight [25] and body mass index (BMI) in renal tubulointerstitium in DN patients was performed.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36978091", "locator": "sections[7] \"Statistical analysis\" paragraph 2", "quote": "Also, Pearson correlation analysis between transcription factor genes and glomerular filtration rate (GFR) [17, 25], serum creatine level (SCR) [24, 25], proteinuria [25], body weight [25] and body mass index (BMI) in renal tubulointerstitium in DN patients was performed."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data used to support the findings of this study are included within the article. The datasets used and analyzed during the current study are available from GEO GSE30122 (http://www.ncbi.nlm.nih.gov/geo). Source code is available at the “Supplementary Information” section (Additional file 1).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36978091", "locator": "sections[24] \"notes\" paragraph 1", "quote": "All data used to support the findings of this study are included within the article. The datasets used and analyzed during the current study are available from GEO GSE30122 (http://www.ncbi.nlm.nih.gov/geo). Source code is available at the “Supplementary Information” section (Additional file 1)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 38 transcription factor genes were identified from 166 differentially expressed genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36978091", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "A total of 38 transcription factor genes based on 166 differentially expressed genes (DEGs) were identified by UCSC_TFBS."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 38 transcription factor genes were identified from 166 differentially expressed genes.", "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:36978091"], "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:GSE30122"], "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:GSE30122"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36978091", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12967-023-04069-8", "sha256": "sha256:0523c00399a356887baff4dd30b2ef5603b763d516c5b8f1a741a3f702e837b5", "bytes": 28063, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12967-023-04069-8", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10053902", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE30122", "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=GSE30122", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE30122", "version": null, "note": "All data used to support the findings of this study are included within the article. The datasets used and analyzed during the current study are available from GEO GSE30122 (http://www.ncbi.nlm.nih.gov/geo). Source code is available at the “Supplementary Information” section (Additional file 1).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data used to support the findings of this study are included within the article. The datasets used and analyzed during the current study are available from GEO GSE30122 (http://www.ncbi.nlm.nih.gov/geo). 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