Identification of the hub genes associated with prostate cancer tumorigenesis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37251946", "kind": "science-record", "revision": 2, "content_hash": "sha256:595edd1d5623d1c734030c3ac35e90c8333a4472e9b59ce28ea293154c586a6b", "created_at": "2026-11-01T19:01:58Z", "updated_at": "2026-11-01T21:30:53Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of the hub genes associated with prostate cancer tumorigenesis.", "doi": "10.3389/fonc.2023.1168772", "pmid": "37251946", "authors": ["Honghui Zhu", "Qi Lin", "Xiaomin Gao", "Xixi Huang"], "journal": "Frontiers in oncology", "year": 2023, "abstract": "Introduction: Prostate cancer (PCa) is one of the most common malignant tumors of the male urogenital system; however, the underlying mechanisms remain largely unclear. This study integrated two cohort profile datasets to elucidate the potential hub genes and mechanisms in PCa.\nMethods and Results: Gene expression profiles GSE55945 and GSE6919 were filtered from the Gene Expression Omnibus (GEO) database to obtain 134 differentially expressed genes (DEGs) (14 upregulated and 120 downregulated) in PCa. Gene Ontology and pathway enrichment were performed using the Database for Annotation, Visualization, and Integrated Discovery, showing that these DEGs were mainly involved in biological functions such as cell adhesion, extracellular matrix, migration, focal adhesion, and vascular smooth muscle contraction. The STRING database and Cytoscape tools were used to analyze protein-protein interactions and identify 15 hub candidate genes. Violin plot, boxplot, and prognostic curve analyses were performed using Gene Expression Profiling Interactive Analysis, which identified seven hub genes, including upregulated expressed SPP1 and downregulated expressed MYLK, MYL9, MYH11, CALD1, ACTA2, and CNN1 in PCa compared with normal tissue. Correlation analysis was performed using the OmicStudio tools, which showed that these hub genes were moderately to strongly correlated with each other. Finally, quantitative reverse transcription PCR and western blotting were performed to validate the hub genes, showing that the abnormal expression of the seven hub genes in PCa was consistent with the analysis results of the GEO database.\nDiscussion: Taken together, MYLK, MYL9, MYH11, CALD1, ACTA2, SPP1, and CNN1 are hub genes significantly associated with PCa occurrence. These genes are abnormally expressed, leading to the formation, proliferation, invasion, and migration of PCa cells and promoting tumor neovascularization. These genes may serve as potential biomarkers and therapeutic targets in patients with PCa.", "claims": [{"id": "claim-method", "statement": "Gene expression profiles were analyzed by GEO2R to identify differentially expressed genes in PCa and normal tissues. Finally, genes were annotated using an annotation table downloaded from the GEO website. An absolute value of log2FC (fold change) > 1 and P < 0.05 were used as the screening conditions for DEGs.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37251946", "locator": "sections[4] \"Data processing and DEG screening\" paragraph 2", "quote": "Gene expression profiles were analyzed by GEO2R to identify differentially expressed genes in PCa and normal tissues. Finally, genes were annotated using an annotation table downloaded from the GEO website. An absolute value of log2FC (fold change) > 1 and P < 0.05 were used as the screening conditions for DEGs."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/supplementary material. Further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37251946", "locator": "sections[19] \"Data availability statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/supplementary material. Further inquiries can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 134 common DEGs were screened, including 14 upregulated and 120 downregulated genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37251946", "locator": "sections[11] \"Identification of DEGs\" paragraph 2", "quote": "A total of 134 common DEGs were screened, including 14 upregulated and 120 downregulated genes ( Figure 1C )."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 134 common DEGs were screened, including 14 upregulated and 120 downregulated 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:37251946"], "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:GSE55945"], "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:GSE55945"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37251946", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fonc.2023.1168772", "sha256": "sha256:9a8c9f8384b9a3fadcf42d0167c3def3afc00ba6079e6879595f85c47c22ee23", "bytes": 52324, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fonc.2023.1168772", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10213256", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE55945", "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=GSE55945", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE55945", "version": null, "note": "The original contributions presented in the study are included in the article/supplementary material. Further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/supplementary material. 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