Investigation of hub genes involved in diabetic nephropathy using biological informatics methods.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33145306", "kind": "science-record", "revision": 6, "content_hash": "sha256:3713bad2dac792de23a5f9a184a05f544b8fbe1de81a1e7ffbef13ce0d2965cf", "created_at": "2026-11-01T15:41:14Z", "updated_at": "2026-11-01T22:02:27Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Investigation of hub genes involved in diabetic nephropathy using biological informatics methods.", "doi": "10.21037/atm-20-5647", "pmid": "33145306", "authors": ["Zhanting Li", "Jianxin Liu", "Weiwei Wang", "Yunchun Zhao", "Dengfeng Yang", "Xiaodong Geng"], "journal": "Annals of translational medicine", "year": 2020, "abstract": "BACKGROUND: The aim of this study was to find genes with significantly aberrant expression in diabetic nephropathy (DN) and determine their underlying mechanisms.\nMETHODS: GSE30528 and GSE1009 were obtained by querying the Gene Expression Omnibus (GEO) database. The difference in target gene expression between normal renal tissues and kidney tissues in patients with DN was screened by using the GEO2R tool. Using the Database for Annotation, Visualization, and Integrated Discovery (DAVID) database, differentially expressed genes (DEGs) were analysed by Gene Ontology (GO) annotation and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment. Then, the protein-protein interactions (PPIs) of DEGs were analyzed by Cytoscape with the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database, and the hub genes in this PPI network were recognized by centrality analysis.\nRESULTS: There were 110 genes with significant expression differences between normal and DN tissues. The differences in gene expression involved many functions and expression pathways, such as the formation of the extracellular matrix and the construction of the extracellular domain. The correlation analysis and subgroup analysis of 14 hub genes and the clinical characteristics of DN showed that CTGF, ALB, PDPN, FLT1, IGF1, WT1, GJA1, IGFBP2, FGF9, BMP2, FGF1, BMP7, VEGFA, and TGFBR3 may be involved in the progression of DN.\nCONCLUSIONS: We confirmed the differentially expressed hub genes and other genes which may be the novel biomarker and target candidates in DN.", "claims": [{"id": "claim-method", "statement": "Pearson’s correlation analysis between hub genes, glomerular filtration rate (GFR), and proteinuria in patients with DN was performed using Nephroseq v5 online platform (http://v5.nephroseq.org). Comparisons between two groups were performed using an unpaired Student’s t-test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33145306", "locator": "sections[7] \"Statistical analysis\" paragraph 2", "quote": "Pearson’s correlation analysis between hub genes, glomerular filtration rate (GFR), and proteinuria in patients with DN was performed using Nephroseq v5 online platform (http://v5.nephroseq.org). Comparisons between two groups were performed using an unpaired Student’s t-test."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:33145306"], "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:GSE1009"], "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:GSE1009"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33145306", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/atm-20-5647", "sha256": "sha256:6114168cff361aa04f3b006e03870e7ffaca40ee80f30e879fea267b3d06a9df", "bytes": 29096, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21037/atm-20-5647", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7575993", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE1009", "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=GSE1009", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE1009", "version": null, "note": "The GSE30528 microarray data package contained 22 samples of human glomerular tissue. 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Further analysis of the specific composition showed that it included 9 DN kidney tissue samples and 13 control group kidney tissue samples.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM15965", "GSM15966", "GSM15967", "GSM15968", "GSM15969", "GSM15970"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "8300", "taxon": "Homo sapiens", "title": "Diabetic nephropathy", "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:GSE30528", "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=GSE30528", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE30528", "version": null, "note": "The GSE30528 microarray data package contained 22 samples of human glomerular tissue. The study samples were taken from healthy human transplant donors, diagnostic renal biopsies, and post-nephrectomy specimens. Further analysis of the specific composition showed that it included 9 DN kidney tissue samples and 13 control group kidney tissue samples.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The GSE30528 microarray data package contained 22 samples of human glomerular tissue. The study samples were taken from healthy human transplant donors, diagnostic renal biopsies, and post-nephrectomy specimens. Further analysis of the specific composition showed that it included 9 DN kidney tissue samples and 13 control group kidney tissue samples.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM756992", "GSM756993", "GSM756994", "GSM756995", "GSM756996", "GSM756997", "GSM756998", "GSM756999", "GSM757000", "GSM757001", "GSM757002", "GSM757003", "GSM757004", "GSM757005", "GSM757006", "GSM757007", "GSM757008", "GSM757009", "GSM757010", "GSM757011", "GSM757012", "GSM757013"], "sample_count": 22, "group_sizes": null, "group_sizes_basis": null, "platform": "571", "taxon": "Homo sapiens", "title": "Transcriptome Analysis of Human Diabetic Kidney Disease (DKD Glomeruli vs. Control Glomeruli)", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:33145306:1", "role": "table", "format": "jats-table", "media_type": 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