Integrated analysis of hub genes and intrinsically disordered regions in triple-negative breast cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39674628", "kind": "science-record", "revision": 3, "content_hash": "sha256:a9deb956eb3085e0131320e97a0e3bb6eee265741c6a7ba27469c469598cca8c", "created_at": "2026-11-01T20:29:58Z", "updated_at": "2026-11-01T22:13:19Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated analysis of hub genes and intrinsically disordered regions in triple-negative breast cancer.", "doi": "10.1016/j.jgeb.2024.100408", "pmid": "39674628", "authors": ["Azhar Iqbal", "Faisal Ali", "Sulaiman Ali Alharbi", "Muhammad Sajid", "Saleh Alfarraj", "Momina Hussain", "Tehmina Siddique", "Rakhshanda Mustaq", "Fakhra Shafique", "Muhammad Sarfaraz Iqbal"], "journal": "Journal, genetic engineering & biotechnology", "year": 2024, "abstract": "Triple-negative breast cancer (TNBC) is the most prevalent breast cancer subtype. Its prognosis is poor because there are no effective treatment targets. Despite several attempts, the molecular pathways of TNBC remain unknown, posing a significant clinical barrier in the search for viable targets. Two microarray datasets were used to identify possible targets for TNBC, GSE38959 and GSE45827, retrieved from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) in TNBC samples compared with normal samples were identified using the GEO2R program. KEGG pathway enrichment and Gene Ontology functions were assessed for DEG pathways and functional annotation using ShinyGO 0.77. The STRING database and Cytoscape program were used for protein-protein interaction (PPI) analysis. Furthermore, we evaluated the predictive significance of hub gene expression in TNBC patients using the GEPIA2 online tool. We developed a comprehensive technique to assess whether intrinsically disordered regions (IDRs) are present in the TNBC hub genes. There were 48 DEGs were identified, all of which were upregulated. A putative protein complex containing these four core genes was selected for further analysis. Breast cancer patients with TTK, TOP2A, CENPF, and CCNA2 upregulation had a poor prognosis; TTK and CCNA2 were partially disordered, whereas TOP2A and CENPF were primarily disordered, according to IDR analysis. According to our study, TOP2A and CENPF may be useful therapeutic targets for disruption of the TNBC PPI network.", "claims": [{"id": "claim-method", "statement": "Individuals with TNBC who had high hub gene expression had worse overall survival rates according to the Kaplan-Meier study (Fig. 6).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39674628", "locator": "sections[18] \"High gene expression revealed lower overall survival\" paragraph 2", "quote": "Individuals with TNBC who had high hub gene expression had worse overall survival rates according to the Kaplan-Meier study (Fig. 6)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The gene expression profiles of GSE45827 and GSE38959 in tissues classified as TNBC and non-TNBC were retrieved from the NCBI-GEO11; which is a publicly accessible database containing a collection of microarray data. GSE38959 dataset contained thirty TNBC and 13 standard samples. And GSE45827 dataset contained 41 TNBC and 11 standard samples.12", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39674628", "locator": "sections[3] \"Dataset selection\" paragraph 2", "quote": "The gene expression profiles of GSE45827 and GSE38959 in tissues classified as TNBC and non-TNBC were retrieved from the NCBI-GEO11; which is a publicly accessible database containing a collection of microarray data. GSE38959 dataset contained thirty TNBC and 13 standard samples. And GSE45827 dataset contained 41 TNBC and 11 standard samples.12"}], "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:39674628"], "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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