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pmid:31598425
Identification of potential biomarkers and pivotal biological pathways for prostate cancer using bioinformatics analysis methods.
Zihao He · Xiaolu Duan · Guohua Zeng
PeerJ · 2019 doi:10.7717/peerj.7872
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Experiment
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Analysis
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Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31598425", "kind": "science-record", "revision": 8, "content_hash": "sha256:4e9c9b6c1cf7135aad9f03e87f8456d2294381cb81b586eea87b647574b87147", "created_at": "2026-11-01T15:40:50Z", "updated_at": "2026-11-01T22:44:15Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of potential biomarkers and pivotal biological pathways for prostate cancer using bioinformatics analysis methods.", "doi": "10.7717/peerj.7872", "pmid": "31598425", "authors": ["Zihao He", "Xiaolu Duan", "Guohua Zeng"], "journal": "PeerJ", "year": 2019, "abstract": "BACKGROUND: Prostate cancer (PCa) is a common urinary malignancy, whose molecular mechanism has not been fully elucidated. We aimed to screen for key genes and biological pathways related to PCa using bioinformatics method.\nMETHODS: Differentially expressed genes (DEGs) were filtered out from the GSE103512 dataset and subjected to the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. The protein-protein interactions (PPI) network was constructed, following by the identification of hub genes. The results of former studies were compared with ours. The relative expression levels of hub genes were examined in The Cancer Genome Atlas (TCGA) and Oncomine public databases. The University of California Santa Cruz Xena online tools were used to study whether the expression of hub genes was correlated with the survival of PCa patients from TCGA cohorts.\nRESULTS: Totally, 252 (186 upregulated and 66 downregulated) DEGs were identified. GO analysis enriched mainly in \"oxidation-reduction process\" and \"positive regulation of transcription from RNA polymerase II promoter\"; KEGG pathway analysis enriched mostly in \"metabolic pathways\" and \"protein digestion and absorption.\" Kallikrein-related peptidase 3, cadherin 1 (CDH1), Kallikrein-related peptidase 2 (KLK2), forkhead box A1 (FOXA1), and epithelial cell adhesion molecule (EPCAM) were identified as hub genes from the PPI network. CDH1, FOXA1, and EPCAM were validated by other relevant gene expression omnibus datasets. All hub genes were validated by both TCGA and Oncomine except KLK2. Two additional top DEGs (ABCC4 and SLPI) were found to be associated with the prognosis of PCa patients.\nCONCLUSIONS: This study excavated the key genes and pathways in PCa, which might be biomarkers for diagnosis, prognosis, and potential therapeutic targets.", "claims": [{"id": "claim-method", "statement": "The DEGs were filtered using the limma R package (criteria: adjusted P < 0.05 and |log2 fold change| ≥ 1).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31598425", "locator": "sections[10] \"Data processing and screening of DEGs\" paragraph 2", "quote": "The DEGs were filtered using the limma R package (criteria: adjusted P < 0.05 and |log2 fold change| ≥ 1)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The following information was supplied regarding data availability:\nData is available at NCBI GEO: GSE103512.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31598425", "locator": "sections[27] \"Data Availability Statement\" paragraphs 1-3", "quote": "The following information was supplied regarding data availability:\nData is available at NCBI GEO: GSE103512."}], "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:31598425"], "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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{"label": "Table 1", "caption": "Top 10 upregulated and downregulated DEGs between PCa and NP tissues.", "rows": [["Gene symbol", "Log2FC", "adj.P.Val", "State"], ["NPY", "−3.362711603", "0.000789175", "Upregulated"], ["TARP", "−3.206862002", "4.85E-09", "Upregulated"], ["OR51E2", "−2.828448822", "7.28E-05", "Upregulated"], ["NKX3-1", "−2.528690546", "3.58E-12", "Upregulated"], ["MSMB", "−2.517978536", "5.11E-06", "Upregulated"], ["ACPP", "−2.474802744", "2.29E-09", "Upregulated"], ["SLC45A3", "−2.46284327", "2.66E-08", "Upregulated"], ["C15orf21", "−2.327851135", "0.003615423", "Upregulated"], ["ABCC4", "−2.261776258", "1.46E-08", "Upregulated"], ["LOC100287445", "−2.170028348", "0.000544702", "Upregulated"], ["FOLR1", "3.005860886", "8.83E-09", "Downregulated"], ["KRT13", "2.958317838", "2.03E-08", "Downregulated"], ["SEMG1", "2.881097184", "0.001633121", "Downregulated"], ["SEMG2", "2.444264593", "0.00246384", "Downregulated"], ["OLFM4", "2.410939695", "0.000494142", 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