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pmid:33630978
Identification of UBE2C as hub gene in driving prostate cancer by integrated bioinformatics analysis.
Yan Wang · Jili Wang · Qiusu Tang · Guoping Ren
PloS one · 2021 doi:10.1371/journal.pone.0247827
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Experiment
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Complete file
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Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were performed to identify the function of DEGs. Using STRING and Cytoscape (version 3.7.1), we constructed a protein-protein interaction (PPI) network and identified the hub gene of prostate cancer. Clinical data on GSE70770 and TCGA was collected to show the role of hub gene in prostate cancer progression. The correlations between hub gene and clinical parameters were also indicated by cox regression analysis. Gene Set Enrichment Analysis (GSEA) was performed to highlight the function of Ubiquitin-conjugating enzyme complex (UBE2C) in prostate cancer.\nRESULTS: 243 upregulated genes and 298 downregulated genes that changed in at least two microarrays have been identified. GO and KEGG analysis indicated significant changes in the oxidation-reduction process, angiogenesis, TGF-beta signaling pathway. UBE2C, PDZ-binding kinase (PBK), cyclin B1 (CCNB1), Cyclin-dependent kinase inhibitor 3 (CDKN3), topoisomerase II alpha (TOP2A), Aurora kinase A (AURKA) and MKI67 were identified as the candidate hub genes, which were all correlated with prostate cancer patient' disease-free survival in TCGA. In fact, only UBE2C was highly expressed in prostate cancer when compared with benign prostate tissue in TCGA and the expression of UBE2C was also in parallel with the Gleason score of prostate cancer. Cox regression analysis has indicated UBE2C could function as the independent prognostic factor of prostate cancer. GSEA showed UBE2C had played an important role in the pathway of prostate cancer, such as NOTCH signaling pathway, WNT-β-catenin signaling pathway.\nCONCLUSIONS: UBE2C was pivotal for the progression of prostate cancer and the level of UBE2C was important to predict the prognosis of patients.", "claims": [{"id": "claim-data-access", "statement": "All relevant data are available from the NCBI Gene Expression Omnibus (accession numbers GSE3325, GSE46602, GSE70770, GSE69223, GSE104749, GSE116918).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33630978", "locator": "sections[19] \"Data Availability\" paragraph 2", "quote": "All relevant data are available from the NCBI Gene Expression Omnibus (accession numbers GSE3325, GSE46602, GSE70770, GSE69223, GSE104749, GSE116918)."}], "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:33630978"], "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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