Unveiling Potential Biomarkers for Urinary Tract Infection: An Integrated Bioinformatics Approach.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39224398", "kind": "science-record", "revision": 4, "content_hash": "sha256:83eef8006e7b084e175416c670e6987728333dd392dbf81fd9887883f350fd6d", "created_at": "2026-11-01T20:29:21Z", "updated_at": "2026-11-01T22:55:05Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Unveiling Potential Biomarkers for Urinary Tract Infection: An Integrated Bioinformatics Approach.", "doi": "10.4103/abr.abr_355_23", "pmid": "39224398", "authors": ["Reza Maddah", "Fahimeh Ghanbari", "Maziyar Veisi", "Eman Koosehlar", "Marzieh Shadpirouz", "Zarrin Basharat", "Alireza Hejrati", "Bahareh Shateri Amiri", "Lina Hejrati"], "journal": "Advanced biomedical research", "year": 2024, "abstract": "Background: Urinary tract infections (UTIs) are a widespread health concern with high recurrence rates and substantial economic impact, and they can increase the prevalence of antibiotic resistance. This study employed an integrated bioinformatics approach to identify key genes associated with UTI development, offering potential targets for interventions.\nMaterials and Methods: For this study, the microarray dataset GSE124917 from the Gene Expression Omnibus (GEO) database was selected and reanalyzed. The differentially expressed genes (DEGs) between UTIs and healthy samples were identified using the LIMMA package in R software. In this section, Enrichr database was utilized to perform functional enrichment analysis of DEGs. Subsequently, the protein-protein interaction (PPI) network of the DEGs was constructed and visualized through Cytoscape, utilizing the STRING online database. The identification of hub genes was performed using Cytoscape's cytoHubba plug-in employing various methods. Receiver operating characteristic (ROC) analysis was performed to assess the diagnostic accuracy of hub genes.\nResults: Among the outcomes of the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, the tumor necrosis factor (TNF) signaling pathway was identified as one of the notable pathways. The PPI network of the DEGs was successfully established and visualized in Cytoscape with the aid of the STRING online database. Using cytoHubba with different methods, we identified seven hub genes (STAT1, IL6, IFIT1, IFIT3, IFIH1, MX1, and IRF7). Based on the ROC analysis, all hub genes showed high diagnostic value.\nConclusion: These findings provide a valuable baseline for future research aimed at unraveling the intricate molecular mechanisms behind UTI.", "claims": [{"id": "claim-method", "statement": "To assess the diagnostic effectiveness of these biomarkers, receiver operating characteristic (ROC) curves were generated using GraphPad Prime 9.[16] The area under the ROC curve (AUC) was then calculated, with an AUC value greater than 0.9 indicating that the biomarkers possessed favorable diagnostic value.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39224398", "locator": "sections[6] \"Evaluation of the diagnostic value\" paragraph 2", "quote": "To assess the diagnostic effectiveness of these biomarkers, receiver operating characteristic (ROC) curves were generated using GraphPad Prime 9.[16] The area under the ROC curve (AUC) was then calculated, with an AUC value greater than 0.9 indicating that the biomarkers possessed favorable diagnostic value."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The microarray profile dataset was retrieved from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) databases.[10] The dataset GSE124917, obtained from the Agilent-072363 SurePrint G3 Human GEN v3 8x60K Microarray (GPL21185), consisted of a total of six samples. This dataset included three normal samples and three samples infected with UPEC.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39224398", "locator": "sections[3] \"Source of data and analysis\" paragraph 2", "quote": "The microarray profile dataset was retrieved from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) databases.[10] The dataset GSE124917, obtained from the Agilent-072363 SurePrint G3 Human GEN v3 8x60K Microarray (GPL21185), consisted of a total of six samples. This dataset included three normal samples and three samples infected with UPEC."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Notably, based on the ROC analysis, all hub genes exhibited high diagnostic values with AUC values exceeding 0.9.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39224398", "locator": "sections[11] \"Evaluation of the diagnostic value\" paragraph 2", "quote": "Notably, based on the ROC analysis, all hub genes exhibited high diagnostic values with AUC values exceeding 0.9."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Notably, based on the ROC analysis, all hub genes exhibited high diagnostic values with AUC values exceeding 0.9.", "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:39224398"], "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:GSE124917"], "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:GSE124917"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39224398", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.4103/abr.abr_355_23", "sha256": "sha256:597b3393ff4985ee9a8bbc7cde03483d231299a33771da3de6b937ca6b56ffe2", "bytes": 24087, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.4103/abr.abr_355_23", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11368229", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE124917", "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=GSE124917", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE124917", "version": null, "note": "The microarray profile dataset was retrieved from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) databases.[10] The dataset GSE124917, obtained from the Agilent-072363 SurePrint G3 Human GEN v3 8x60K Microarray (GPL21185), consisted of a total of six samples. 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