Identification and preliminary analysis of hub genes associated with bladder cancer progression by comprehensive bioinformatics analysis.

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It is necessary to understand the molecular mechanisms of the development and progression of BC to determine treatment options. Publicly available expression data were obtained from TCGA and GEO databases to spot differentially expressed genes (DEGs) between cancer and normal bladder tissues. Weighted co-expression networks were constructed, and Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed. Associations in hub genes, immune infiltration, and immune therapy were evaluated separately. Protein-protein interaction (PPI) networks for the genes identified in the normal and tumor groups were launched. 3461 DEGs in the TCGA dataset and 1069 DEGs in the GSE dataset were identified, including 87 overlapping genes between cancer and normal bladder groups. Hub genes in the tumor group were mainly enriched for cell proliferation, while hub genes in the normal group were related to the synthesis and secretion of neurotransmitters. Based on survival analysis, CDH19, RELN, PLP1, and TRIB3 were considerably associated with prognosis (P < 0.05). CDH19, RELN, PLP1, and TRIB3 may play important roles in the development of BC and are potential biomarkers in therapy and prognosis.", "claims": [{"id": "claim-method", "statement": "Similarly, the prognostic value of each hub gene was further evaluated using the survival package in R based on TCGA and GEO data.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38307969", "locator": "sections[8] \"Validation of the prognostic value and expression of hub genes\" paragraph 2", "quote": "Similarly, the prognostic value of each hub gene was further evaluated using the survival package in R based on TCGA and GEO data."}], "state": "complete"}, {"id": "claim-data-access", "statement": "RNA-sequencing profiles and clinical characteristics for patients with BC were obtained from TCGA (https://portal.gdc.cancer.gov/), and the GSE13507 dataset was downloaded from GEO (https://www.ncbi.nlm.nih.gov/gds).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38307969", "locator": "sections[34] \"Data availability\" paragraph 2", "quote": "RNA-sequencing profiles and clinical characteristics for patients with BC were obtained from TCGA (https://portal.gdc.cancer.gov/), and the GSE13507 dataset was downloaded from GEO (https://www.ncbi.nlm.nih.gov/gds)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Survival analysis identified CDH19, RELN, PLP1, and TRIB3 as genes associated with bladder cancer prognosis.", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "Based on survival analysis, CDH19, RELN, PLP1, and TRIB3 were considerably associated with prognosis (P < 0.05)."}, "evidence": [{"asset": "source:pmid:38307969", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Based on survival analysis, CDH19, RELN, PLP1, and TRIB3 were considerably associated with prognosis (P < 0.05)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Survival analysis identified CDH19, RELN, PLP1, and TRIB3 as genes associated with bladder cancer prognosis.", "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:38307969"], "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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