Risk score based on three mRNA expression predicts the survival of bladder cancer.

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By utilizing the gene expression in The Cancer Genome Atlas (TCGA) dataset, and another two datasets, in GSE13507 and GSE31684, we constructed a risk score staging system with Cox multivariate regression to evaluate predict the outcome of BLCA patients. Three genes consist of RCOR1, ST3GAL5, and COL10A1 were used to predict the survival of BLCA patients. The patients with low risk score have a better survival rate than those with high risk score, significantly. The survival profiles of another two datasets (GSE13507 and GSE31684), which were used for candidate gene selection, were similar as the training dataset (TCGA). Furthermore, survival prediction effect of risk score staging system in another 2 independent datasets, GSE40875 and E-TABM-4321, were also validated. Compared with other clinical observations, and the risk score performs better in evaluating the survival of BLCA patients. Moreover, the correlation between radiation were also evaluated, and we found that patients have a poor survival in high risk group, regardless of radiation. Gene Set Enrichment Analysis was also implemented to find the difference between high-risk and low-risk groups on biological pathways, and focal adhesion and JAK signaling pathway were significantly enriched. In summary, we developed a risk staging model for BLCA patients with three gene expression. The model is independent from and performs better than other clinical information.", "claims": [{"id": "claim-method", "statement": "The significantly altered signaling pathways between high risk group and the low risk group were assessed with Gene Set Enrichment Analysis (GSEA) to investigate why the risk score predicts the survival of BLCA patients.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28977887", "locator": "sections[7] \"Altered pathways in the high risk score patients\" paragraph 2", "quote": "The significantly altered signaling pathways between high risk group and the low risk group were assessed with Gene Set Enrichment Analysis (GSEA) to investigate why the risk score predicts the survival of BLCA patients."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The TCGA dataset were downloaded from UCSC Xena website (http://xena.ucsc.edu/), the expression value were converted to normalized RSEM values, the detailed pre-processing steps, including mapping and normalization, were described on UCSC Xena website.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28977887", "locator": "sections[10] \"Data pre-processing\" paragraph 2", "quote": "The TCGA dataset were downloaded from UCSC Xena website (http://xena.ucsc.edu/), the expression value were converted to normalized RSEM values, the detailed pre-processing steps, including mapping and normalization, were described on UCSC Xena website."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study constructed a bladder-cancer survival risk score using Cox multivariate regression applied to gene-expression data from TCGA-BLCA, GSE13507, and GSE31684.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:28977887", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "By utilizing the gene expression in The Cancer Genome Atlas (TCGA) dataset, and another two datasets, in GSE13507 and GSE31684, we constructed a risk score staging system with Cox multivariate regression to evaluate predict the outcome of BLCA patients."}, {"asset": "source:pmid:28977887", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Three genes consist of RCOR1, ST3GAL5, and COL10A1 were used to predict the survival of BLCA patients."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study constructed a bladder-cancer survival risk score using Cox multivariate regression applied to gene-expression data from TCGA-BLCA, GSE13507, and GSE31684.", "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:28977887"], "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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